Avian Flu Regulations in New York: What Every Poultry Owner Must Know

New York has been one of the most actively regulated states in the country when it comes to avian influenza. Since February 2022, the state has confirmed HPAI in dozens of flocks, triggered emergency market shutdowns, and rolled out a layered system of biosecurity mandates, movement restrictions, and reporting requirements that apply to everyone from large commercial egg producers to small backyard flock owners.

Whether you raise a dozen chickens in a rural county or operate a licensed live bird market in New York City, understanding avian flu regulations in New York is not optional — it is a legal obligation with real financial and criminal consequences for non-compliance. This guide walks you through every major regulatory layer, from how the virus is classified to what happens if your flock tests positive.

HPAI vs. LPAI: Understanding Avian Flu Classifications in New York

Not all avian influenza strains carry the same regulatory weight. New York’s response framework — and the specific rules you must follow — depends heavily on which classification of avian influenza is involved. Understanding the distinction between HPAI and LPAI is the foundation for everything else in this guide.

Low Pathogenic Avian Influenza (LPAI) refers to strains that typically cause mild or no clinical symptoms in birds. While LPAI can still trigger regulatory action, especially for H5 and H7 subtypes that have the potential to mutate into HPAI strains, the response is generally less aggressive than for confirmed HPAI cases. To protect U.S. poultry from HPAI and stop trade interruptions, federal, state, and industry officials must cooperate to actively prevent and control LPAI, since controlling LPAI prevents HPAI infections.

Highly Pathogenic Avian Influenza (HPAI) is a far more serious designation. Avian influenza is caused by an influenza type A virus carried by free-flying wild birds such as ducks, geese, gulls, and shorebirds. Generally, influenza viruses can infect some wild species without causing signs of disease, but new strains can emerge that cause illness with high mortality in both wild birds and domestic poultry — these are designated as HPAI.

The strain currently driving New York’s outbreak is H5N1 clade 2.3.4.4b. What sets this strain apart from previous strains of avian influenza is the scale of its impact on migratory birds and how easily it jumps from species to species — in just four years, this H5N1 strain of HPAI has swept the globe pole-to-pole.

From a regulatory standpoint, a confirmed HPAI detection on your premises triggers the most aggressive state and federal response: mandatory depopulation, quarantine zones, movement restrictions, and a structured indemnity process. An LPAI H5 or H7 detection also triggers mandatory reporting and testing requirements under New York’s live bird marketing system rules, but the immediate response steps differ in severity.

Premises Registration Requirements for Poultry Owners in New York

Before any biosecurity rules or movement restrictions apply, you need to understand whether your operation must be registered with the state. New York uses a layered registration framework that applies differently depending on your operation type.

Domestic Animal Health Permits are a core requirement for anyone buying or selling poultry in New York. The Department of Agriculture and Markets is concerned with animal disease control and traceability in all animals, including poultry. To provide adequate control of infectious and communicable diseases, permits are issued to those who deal in, handle, and transport domestic animals. Any person who buys or sells poultry is an animal dealer and must have a Domestic Animal Health Permit.

National Poultry Improvement Plan (NPIP) Participation is a voluntary federal-state cooperative program, but it is effectively required for many commercial transactions in New York. The National Poultry Improvement Program (NPIP) is a voluntary state-federal cooperative testing and certification program for poultry breeding flocks, baby chicks, poults, hatching eggs, hatcheries, and dealers. If you are importing hatching eggs or day-old chicks into the state, NPIP certification is not optional in practice.

All hatching eggs and day-old poultry imported into New York State must be from a flock that is certified US Pullorum-Typhoid Clean and US H5/H7 Avian Influenza Clean (or US Avian Influenza Clean).

Live Bird Market Authorization carries its own licensing layer. Only authorized poultry dealers may deliver poultry to New York live bird markets. If you operate in or supply the live bird marketing system, you must call AGM at (518) 457-3502 for the specific requirements that apply to your operation. In addition to New York State import requirements, animals whose destination is within New York City may be subject to New York City Department of Health and Mental Hygiene regulations, and poultry entering New York City for any reason must meet these regulations.

Biosecurity Requirements for Commercial and Backyard Flocks in New York

Biosecurity is the cornerstone of New York’s avian flu prevention strategy. The state’s requirements apply to all poultry owners, though the depth of compliance expected scales with the size and commercial nature of your operation.

AGM encourages those involved in poultry production to practice good biosecurity measures and take extra steps to prevent their flocks from becoming infected. All poultry producers, from small backyard to large commercial operations, should review their biosecurity plans and take precautions to protect their birds.

Core biosecurity practices required or strongly recommended by AGM include:

• Discouraging unnecessary visitors, using biosecurity signs to warn people not to enter buildings without permission, and asking all visitors if they have had any contact with any birds in the past five days. Entry should be forbidden to employees and visitors who own any kind of fowl.
• Requiring all visitors to cover and disinfect all footwear, locking all entrances to chicken houses after hours, and avoiding non-essential vehicular traffic on-farm.
• After hauling birds to processors, cleaning and disinfecting poultry transport coops and vehicles before they return to the farm.
• Keeping birds away from wild ducks and geese and their droppings.

For commercial operations, the requirements go further. Upon hire, all personnel who work in a market must be trained in biosecurity procedures by animal health officials or by a trained company representative, and the premises must keep a record of employee training on file for at least 12 months.

If your commercial operation has been previously confirmed positive for HPAI, biosecurity audits become a legal condition for restocking and maintaining indemnity eligibility. Commercial poultry premises are required to successfully pass a biosecurity audit prior to restocking if they were previously HPAI-infected and wish to be eligible for indemnity for the restocked poultry.

The good news is that financial assistance is available. Commercial poultry farms with more than 500 birds are eligible to receive cost-share funds. USDA covers up to 75% of the cost to repair the highest-risk biosecurity issues identified by the assessment, with the grower responsible for the remaining 25%. The maximum reimbursement ranges from $2,500 to $25,000 depending on the size of the flock and type of bird being raised.

Reporting Sick or Dead Birds in New York

Prompt reporting is one of the most legally significant obligations you have as a poultry owner in New York. Delayed or missed reporting can expose you to penalties, void your indemnity eligibility, and allow the virus to spread to neighboring flocks.

Diseases need to be reported to the Department when they meet certain criteria. For avian influenza specifically, any unusual mortality event or clinical signs consistent with HPAI — including sudden death, severe respiratory distress, neurological signs, or a sharp drop in egg production — must be reported to AGM immediately. You should not wait for a laboratory confirmation before making the call.

Who to call depends on what you are reporting:

• Sick or dead poultry on your premises: Contact the New York State Department of Agriculture and Markets at (518) 457-3502.
• Sick or dead wild birds in a public area: New Yorkers who spot a sick or dead bird should maintain a safe distance and report the sighting. For poultry, call the New York State Department of Agriculture and Markets.
• Wild bird die-offs: To strengthen surveillance in New York, NYSDEC recently launched a public reporting form, though public health officials warn people against handling sick or dead animals.

When reporting, be prepared to describe the number of birds affected, the species, the onset of symptoms, and any recent changes to your flock’s exposure — such as new birds introduced, visitors, or contact with wild waterfowl. AGM will dispatch an animal health inspector to conduct testing if warranted.

For those working in or around live bird markets, individuals working in the markets will be assessed for potential high-risk exposure and monitored for symptoms by the New York City Department of Health and Mental Hygiene. If any become ill, they will be evaluated for infection with avian influenza.

Understanding avian tuberculosis and avian chlamydiosis is also worthwhile, as these are other reportable avian diseases in New York that share some clinical signs with avian influenza and may require simultaneous investigation.

New York’s Current HPAI Status and Active Outbreak Zones

New York has been dealing with a persistent, multi-year HPAI outbreak since February 2022. The situation has evolved significantly, with new detections continuing into 2025 and 2026.

As of March 31, 2026, 80 flocks in New York State have tested positive for HPAI since February 2022. The Department is working closely with USDA APHIS on a joint incident response and is also collaborating with partners at the Department of Health and Department of Environmental Conservation.

The most acute phase of the current outbreak involved New York City’s live bird market system. This followed seven detections of avian influenza in markets in Queens, the Bronx, and Brooklyn during routine surveillance conducted by AGM since January 31, 2025. The state responded with a sweeping emergency order. In February 2025, a series of H5N1 detections across the city prompted Governor Kathy Hochul to temporarily shut down all live bird markets for depopulation and disinfection. But even that sweeping intervention failed to stop the problem, and in the year since, official reports of bird flu from these facilities have continued to rise, as have cases in wild birds and an increasing number of wild mammals.

Wild bird surveillance paints an equally concerning picture. The Wildlife Health Program began receiving reports of larger mortality events involving 20 or more birds in Regions 3 and 8 in the fall of 2025, with cases spiking in early December and a steadily increasing number of calls from the public about suspected and confirmed HPAI birds. H5N1 has been found in nearly 290 birds across 35 species, with waterfowl and raptors being the most affected.

The virus has also crossed into mammals. In addition to wild birds, HPAI has been confirmed in wild mammals in New York, with over 30 cases across eight species, including red foxes, raccoons, a striped skunk, a Virginia opossum, and a bobcat. New York recently had the first confirmed positive cases of HPAI in an Eastern gray squirrel and a muskrat.

Avian influenza virus infections follow a seasonal pattern tied to bird migration, with cases peaking in late fall and winter. This means that if you are reading this during or approaching migration season, your biosecurity vigilance should be at its highest level.

Poultry Movement and Quarantine Restrictions in New York

New York maintains some of the most detailed poultry movement rules in the northeastern United States. These rules apply at the state border, within the live bird marketing system, and around any premises where HPAI has been detected.

Importing Poultry into New York

The requirements for importing poultry into New York State for any purpose other than slaughter are: a Certificate of Veterinary Inspection issued within 30 days prior to entry or a USDA VS Form 9-3, and poultry must be from an NPIP US Pullorum-Typhoid Clean flock or be tested for pullorum-typhoid within 90 days prior to entry.

New regulations require that all live poultry moved into New York must be from a source flock in which 30 birds were tested for avian influenza within ten days prior to entry, from a source flock certified by the state of origin as an Avian Influenza Monitored Flock, or from a source flock certified as clean of HPAI under the National Poultry Improvement Plan (NPIP).

Live Bird Market Entry Requirements

If you supply poultry to New York’s live bird marketing system, pre-entry testing requirements are now mandatory and tightly controlled. For purposes of moving poultry into a live bird market, all poultry shall only originate and move from a source flock in which a minimum of 30 birds, or all birds for flocks less than 30 birds, aged seven days or older, have tested negative for avian influenza.

The date of sample collection shall be within 72 hours prior to the date of entry into the New York live bird marketing system, and the shipment must be accompanied by a copy of the finalized laboratory report indicating that the poultry tested negative for avian influenza. All avian influenza testing must be conducted at a National Animal Health Laboratory Network (NAHLN) laboratory.

Movement Restrictions Around Infected Premises

When HPAI is confirmed on a premises, a control area is established. This includes an infected zone immediately around the affected farm and a buffer zone extending at least 7 kilometers beyond it. APHIS requires a biosecurity audit for commercial poultry premises within the buffer zone (minimal 7 km radius around the infected zone) prior to movement of poultry onto the premises if the owner wishes to remain eligible for federal indemnity.

Under the new rule, when a poultry producer intends to move poultry onto a premises located within a buffer zone, the receiving premises in the buffer zone must pass a biosecurity audit. This biosecurity audit will be virtual unless the State Animal Health Officer requests an in-person audit. If the receiving premises passed a biosecurity audit within the immediate prior six months of the date of movement, a new audit is not required.

For those subject to animal movement regulations in other states, it is worth noting that New York’s poultry movement rules are among the most prescriptive in the region, with testing timelines and documentation requirements that must be met before birds cross state lines or enter commercial channels.

Flock Depopulation and Compensation Rules in New York

If HPAI is confirmed on your premises, New York State and USDA will move quickly to contain the outbreak through depopulation — the humane destruction of your entire flock to prevent further spread. Understanding how this process works, and what compensation you may be entitled to, is essential knowledge for any poultry owner.

The Depopulation Process

Once HPAI is confirmed, AGM issues a Notice and Order directing the depopulation of all birds on the affected premises. In one confirmed case in Madison County in February 2025, a backyard poultry flock housing approximately 15 ducks and geese tested positive for H5N1, and as recommended by the NYS Department of Agriculture and Markets, any remaining birds were euthanized in order to prevent further spread.

For live bird markets with confirmed detections, the process involves an accelerated sell-down followed by full depopulation. All live bird markets harboring birds with clinical signs of HPAI shall have no more than three days to sell down all inventory and then shall close for an additional five days following cleaning and disinfection procedures.

After depopulation, the premises must undergo a thorough cleaning and disinfection process. Cleaning and disinfection includes the removal of all organic debris from all equipment, caging, flooring, and requires that all surfaces be cleaned with soap or detergent, rinsed with water, and saturated with a disinfectant appropriate for killing the avian influenza virus, in accordance with the manufacturer’s label.

Federal Indemnity and Compensation

USDA provides indemnity and compensation for losses incurred following a confirmed detection of HPAI on a premise. However, this compensation is not automatic — it comes with conditions that have become more stringent in recent years.

Since the beginning of the current HPAI outbreak in 2022, APHIS has made indemnity payments to over 1,200 producers. Of these, 67 unique commercial poultry premises have had at least two HPAI infections during the current outbreak, including 18 premises infected three or more times. Those with reinfections have received over $365 million in indemnity payments, out of nearly $1.1 billion distributed in total.

To curb repeat infections and protect public funds, USDA’s December 2024 interim final rule tightened eligibility. When a poultry producer intends to restock a previously infected premises, that premises must pass a biosecurity audit prior to the movement of poultry onto the premises. In addition, all previously infected premises must pass a virtual biosecurity audit every six months until the state in which the premises is located declares freedom from HPAI.

Additionally, APHIS will not pay indemnity for flocks moved onto premises in active infected zones if the flocks become infected with HPAI within 14 days following the dissolution of the control area around an active infected premises.

For indemnity valuation, the amount of indemnification depends on federal regulations and federal resources. For established flocks and distribution systems, indemnity for destroyed birds will be based on the birds’ appraised value.

Penalties for Non-Compliance in New York

New York takes avian flu regulation enforcement seriously. Non-compliance with AGM Notices and Orders, testing requirements, movement restrictions, or reporting obligations can expose you to a range of civil and criminal consequences.

State-Level Penalties Under Agriculture and Markets Law

New York’s Agriculture and Markets Law gives AGM broad authority to issue Notices and Orders that carry the force of law. Violations of these orders — including failure to comply with depopulation directives, movement restrictions, or cleaning and disinfection requirements — can result in civil penalties. Under New York Agriculture and Markets Law, violations can carry fines per day of non-compliance, and AGM has the authority to seek injunctive relief to compel compliance.

The state’s authority under Article 5 (Diseases of Livestock) and Part 45 (Avian Influenza) of the Agriculture and Markets regulations means that failure to report a suspected HPAI case, moving restricted birds without authorization, or operating a live bird market in violation of a Notice and Order are all enforceable offenses.

Loss of Indemnity Eligibility as a Financial Penalty

Beyond formal fines, the most significant financial consequence of non-compliance is the loss of your right to federal indemnity payments. A producer who does not make corrections recommended in APHIS’s biosecurity audit will not be eligible for indemnity payments if the premises experiences future infections within the same outbreak.

This means that if you fail to pass or complete a required biosecurity audit — whether for restocking after an infection or for operating in a buffer zone — you bear the full financial cost of any future flock loss without federal assistance. Given that flock values can run into the hundreds of thousands of dollars for commercial operations, this is a severe penalty in practical terms.

Permit Revocation and Market Closure

For live bird market operators and licensed poultry dealers, non-compliance can result in permit revocation. Once birds are in the marketing system, state officials verify test records and monitor sanitation levels at the live bird markets, and employees of the Department’s Division of Animal Industry routinely test poultry in live bird markets for avian influenza. Operators who fail inspections or are found to have introduced untested birds into the system risk losing their authorization to operate entirely.

Federal Enforcement Exposure

Because HPAI response in New York operates as a joint state-federal incident, violations that implicate federal regulations — such as moving poultry across state lines without required health certificates, or introducing birds into commerce in violation of a federal quarantine — can also trigger federal enforcement action under the Animal Health Protection Act, which carries its own civil and criminal penalties.

Staying current on New York’s evolving avian flu regulations requires regular engagement with official sources. Bookmark the AGM Poultry page and the CDC’s A(H5) Bird Flu situation summary for the latest updates. For those managing other regulated animals in New York and surrounding states, our guides on horse boarding regulations in Wisconsin and fishing regulations in New York cover the regulatory landscape for other species and activities under state oversight.

Avian flu regulations in New York are not static — they shift with outbreak conditions, new federal rules, and emergency orders that can take effect within hours. Your best defense is a combination of strong on-farm biosecurity, registered premises, up-to-date testing documentation, and a clear understanding of who to call and what to do the moment something looks wrong with your flock.