New York State Medicaid Coverage Policy and Billing Guidance for the Administration of COVID-19 Vaccines

Updates as of 9-28-2021 are highlighted in yellow

  • Guidance is also available in Portable Document Format (PDF)

This guidance sets forth New York State (NYS) Medicaid´s reimbursement policy for the administration of COVID-19 vaccines approved by the FDA or authorized for emergency use and instructions for providers to bill the cost of administration of authorized COVID-19 vaccine. Information about vaccines receiving EUA by the FDA can be found on the COVID-19 Vaccines web page.

NY Medicaid´s policy for the administration of COVID-19 vaccine will continue to remain in effect in accordance with the Public Readiness and Emergency Preparedness Act (PREP Act). As additional COVID-19 vaccines become available under an EUA, or are otherwise approved by the FDA, this billing guidance will be updated as needed.

I. NYS Medicaid Coverage Policy

This coverage policy applies to both Medicaid fee-for-service (FFS) and Medicaid Managed Care (MMC).

A. NYS Medicaid Will Not Reimburse for the Cost of COVID-19 Vaccine

  1. Payment will not be made to NYS Medicaid providers for the cost of COVID-19 vaccine because the vaccine is available at no cost to providers. Providers must not bill the Current Procedural Terminology (CPT) code for the vaccine.
  2. In order to obtain COVID-19 vaccine at no cost, Medicaid enrolled providers must be legally authorized to administer the vaccine and also enroll as COVID-19 vaccine providers with the Centers for Disease Control and Prevention (CDC), the NYS Department of Health Bureau of Immunization, or the NYC Department of Health and Mental Hygiene (NYCDOHMH) Bureau of Immunization. Such providers are considered qualified providers by the Medicaid program for the purpose of COVID-19 vaccine administration.
  3. For information on how to enroll in the NYS COVID-19 Vaccination Program and how to register for the NYSIIS or CIR, please visit COVID-19 Vaccine Information for Providers.
  4. Note that this program is distinct from the Vaccines for Children (VFC) Program and separate enrollment is required.

B. Reimbursement for Administration of Authorized COVID-19 Vaccines

  1. The NYS Medicaid program, including the Medicaid FFS program and MMC, will reimburse NYS Medicaid enrolled and qualified providers for the administration of COVID-19 vaccines that have been issued an EUA by the FDA for the prevention of COVID-19.
  2. Reimbursement for administration of COVID-19 vaccines may be based on a patient-specific order or non-patient specific order ("standing order"). These orders must be kept on file by the provider. Standing orders enable assessment and vaccination of the patient without the need for clinician examination or a patient-specific order from the attending provider at the time of the patient interaction. For more information, please see:
  3. The ordering provider´s National Provider Identifier (NPI) is required on the Medicaid claim. Ordering providers, including MMC network providers, are required to be enrolled in the NYS Medicaid program.
  4. Providers are prohibited from charging Medicaid members a co-payment or any cost sharing responsibility for the COVID-19 vaccine or the administration of the COVID-19 vaccine.
  5. Providers must not bill NYS Medicaid for the administration of the COVID-19 vaccine to members who are also enrolled in Medicare. Dually eligible enrollees will continue to access full coverage of immunization services through Medicare.

II. NYS Medicaid FFS Billing Instructions and Fees

The following billing instructions and fees apply to Medicaid FFS.

A. Qualified Hospital Outpatient Departments, Federally Qualified Health Centers and Office-Based Practitioners

  1. NYS Medicaid enrolled hospital outpatient departments, free-standing diagnostic and treatment centers (D&TCs), Federally Qualified Heath Centers (FQHCs), and private office-based practitioners can bill NYS Medicaid for COVID-19 vaccine administration administered to NYS Medicaid FFS members in accordance with Table 1 below.
Table 1
CPT Code Manufacturer & COVID-19 Vaccine Administration CPT Code Short Descriptions Fee Effective for Dates of Service on or after: Fee Effective for Dates of Service on or after:
0001A Pfizer-BioNTech - ADM SARSCOV2 30MCG/0.3ML - 1st Dose $13.23 12/11/2020-3/31/2021 $40.00 4/1/2021
0002A Pfizer-BioNTech - ADM SARSCOV2 30MCG/0.3ML - 2nd Dose $13.23 12/11/2020-3/31/2021 $40.00 4/1/2021
0003A Pfizer-BioNTech - ADM SARSCOV2 30MCG/0.3ML - 3rd Dose N/A 8/12//2021 $40.00 8/12/2021
0004A Pfizer-BioNTech - ADM SARSCOV2 30MCG/0.3ML - Booster Dose N/A 9/22//2021 $40.00 9/22/2021
0011A Moderna - ADM SARSCOV2 100MCG/0.5ML - 1st Dose $13.23 12/18/2020-3/31/2021 $40.00 4/1/2021
0012A Moderna - ADM SARSCOV2 100MCG/0.5ML - 2nd Dose $13.23 12/18/2020-3/31/2021 $40.00 4/1/2021
0013A Moderna - ADM SARSCOV2 100MCG/0.5ML - 3rd Dose N/A 8/12//2021 $40.00 8/12/2021
0031A Janssen - ADM SARSCOV2 VAC AD26 .5ML $13.23 2/27/2021-3/31/2021 $40.00 4/1/2021

NOTE: Practitioner and Ordered Ambulatory claims submitted prior to June 1, 2021 for dates of service on or after April 1, 2021 that were paid at $13.23 will be automatically reprocessed at the new $40.00 administration fee. Providers do not need to submit claim adjustments.

  1. Hospital outpatient departments, D&TCs, and FQHCs should bill an ordered ambulatory claim for COVID-19 vaccine administration.
  2. Office-based practitioners should bill a professional claim for COVID-19 vaccine administration.
  3. The COVID-19 vaccine administration CPT codes above include the actual work of administering the vaccine, including all necessary counseling provided to patients and/or caregivers, required vaccination reporting, and updating of electronic records.
  4. NYS Medicaid enrolled providers, if within their scope of practice, can bill an Evaluation and Management (E&M) visit on the same day as the COVID-19 vaccine administration, when additional services are provided that are beyond the components represented in the COVID-19 vaccine administration code, and when all of the key components of the E&M code have been provided and documented.
  5. Hospital outpatient departments, D&TCs, and FQHCs providing comprehensive clinic services in addition to and beyond the scope of the COVID-19 vaccine administration service (see #4 & #6 above) can bill an appropriate APG or PPS claim for the medical services provided and can bill a separate ordered ambulatory claim for the COVID-19 vaccine administration.
  6. When the only service provided is the COVID-19 vaccine administration, only an ordered ambulatory claim for the vaccine administration can be submitted.
  7. Ambulance providers have been assigned Category of Service code (COS) "0282" and should bill a professional claim using the COVID-19 vaccine administration codes in Table 1. Ambulance provider claims for COVID-19 vaccine administration should be identified as a non-emergency service by reporting the "Emergency Indicator" as "N" No prior approval/prior authorization is required.
    NOTE: As of June 25, 2021, with the expiration of the New York State Declared Disaster Emergency, ambulance providers may only bill for Covid-19 vaccinations administered by paramedics.

B. Qualified Pharmacies

The following billing instructions and fees apply to the Medicaid FFS program.

  1. Pharmacies affiliated with a point-of-dispensing (POD) site, such as a skilled nursing facility, residential facility, or mobile vaccination site must have the pharmacy operating site enrolled with NYS Medicaid FFS.

The pharmacy must submit via NCPDP D.0, in the Claim Segment field 436-E1 (Product/Service ID Qualifier), a value of "09" (HCPCS), which qualifies the code submitted in field 407-D7 (Product/Service ID) as a procedure code. In field 407-D7 (Product/Service ID), enter the Procedure code from Table 2 for the appropriate vaccine administration. For example, submit the claim line with the Procedure code "0001A" (Immunization Administration). Do not submit another claim line for the vaccine procedure code as the vaccine is being provided free of charge. Pharmacies will bill with a quantity of "1" and a day supply of "1".

NCPDP D.0 Claim Segment Field Value
436-E1 (Product/Service ID Qualifier) Value of "09" (HCPCS), which qualifies the code submitted in field 407-D7 (Product/Service ID) as a procedure code
407-D7 (Product/Service ID) Enter an applicable procedure code listed in Table 2
442-E7 (Quantity Dispensed) Enter the value of "1" for the procedure administration code in Table 2
405-D5 (Day Supply) Enter the value of "1"

Refer to the NCPDP D.0 Companion Guide.

Table 2
CPT Code Manufacturer & COVID-19 Vaccine Administration CPT Code Short Descriptions Fee Effective for Dates of Service on or after: Fee Effective for Dates of Service on or after:
0001A Pfizer-BioNTech - ADM SARSCOV2 30MCG/0.3ML - 1st Dose $13.23 12/11/2020-3/31/2021 $40.00 4/1/2021
0002A Pfizer-BioNTech - ADM SARSCOV2 30MCG/0.3ML - 2nd Dose $13.23 12/11/2020-3/31/2021 $40.00 4/1/2021
0003A Pfizer-BioNTech - ADM SARSCOV2 30MCG/0.3ML - 3rd Dose N/A 8/12//2021 $40.00 8/12/2021
0004A Pfizer-BioNTech - ADM SARSCOV2 30MCG/0.3ML - Booster Dose N/A 9/22//2021 $40.00 9/22/2021
0011A Moderna - ADM SARSCOV2 100MCG/0.5ML - 1st Dose $13.23 12/18/2020-3/31/2021 $40.00 4/1/2021
0012A Moderna - ADM SARSCOV2 100MCG/0.5ML - 2nd Dose $13.23 12/18/2020-3/31/2021 $40.00 4/1/2021
0013A Moderna - ADM SARSCOV2 100MCG/0.5ML - 3rd Dose N/A 8/12//2021 $40.00 8/12/2021
0031A Janssen - ADM SARSCOV2 VAC AD26 .5ML $13.23 2/27/2021-3/31/2021 $40.00 4/1/2021

NOTE: Pharmacy claims for dates of service on or after April 1, 2021 that were submitted prior to June 1, 2021 and were paid $13.23 will be automatically reprocessed by eMedNY and will pay the $40.00 administration fee. Providers do not need to submit claim adjustments. * If a claim was denied for the administration of a 3rd dose prior to 8/23/2021, the pharmacy will need to re-submit the claim for reimbursement.

  1. Please see the July 2016 Medicaid Update for further guidance on origin code and serial number values that must be submitted on the claim for "Pharmacy dispensing" when applicable for non-patient specific orders. In the origin code use "5" and the corresponding serial number of "99999999" for "Pharmacy dispensing" when applicable for non-patient specific orders.
NCPDP D.0 Claim Segment Field Value
444-E9 (Pharmacist ID) Enter Pharmacist NPI number
411-DB (Prescriber ID) Enter Prescriber NPI number

Updates to procedure codes will be available.

C. Qualified Other Rate-Based Providers

The following billing instructions and fees apply to Medicaid FFS.

  1. The provider types listed below may bill Medicaid FFS and MMC plans for administration of authorized COVID-19 vaccine when administered by provider or facility staff to Medicaid members in a residential or other institutional setting.
  2. The administration fee is in addition to the rate (i.e. per diem, per visit, per hour) reimbursed to the provider and must be billed to Medicaid separately.
  3. Rate-based providers may also bill for COVID-19 vaccine administration on a stand-alone claim when other services are not provided.
  4. The providers identified below have been enrolled under COS 0268 and will be issued the rate codes identified in Table 3 below for billing purposes:
    • Skilled Nursing Facilities (SNFs)
    • Certified Home Health Agencies (CHHAs)
    • Hospice
    • Adult Day Health Care (ADHC)
    • Inpatient Hospitals
    • Voluntary Foster Care Agencies (VFCAs)
    • Assisted Living Programs (ALPs)
Table 3
Rate Code Rate Code Description Fee Effective for Dates of Service on or after: Fee Effective for Dates of Service on or after:
5497 PFIZER - COVID-19 Vaccine Administration – 1st Dose $13.23 12/11/2020-3/31/2021 $40.00 4/1/2021
5498 PFIZER - COVID-19 Vaccine Administration – 2nd Dose $13.23 12/11/2020-3/31/2021 $40.00 4/1/2021
5508 PFIZER - COVID-19 Vaccine Administration - 3rd Dose N/A 8/12//2021 $40.00 8/12/2021
5514 PFIZER - COVID-19 Vaccine Administration - Booster Dose N/A 9/22//2021 $40.00 9/22/2021
5499 MODERNA - COVID-19 Vaccine Administration – 1st Dose $13.23 12/18/2020-3/31/2021 $40.00 4/1/2021
5500 MODERNA - COVID-19 Vaccine Administration – 2nd Dose $13.23 12/18/2020-3/31/2021 $40.00 4/1/2021
5509 MODERNA - ADM SARSCOV2 100MCG/0.5ML - 3rd Dose N/A 8/12//2021 $40.00 8/12/2021
5507 JANSSEN - COVID-19 Vaccine Administration $13.23 2/27/2021-3/31/2021 $40.00 4/1/2021

NOTE: Rate-based claims for dates of service on or after April 1, 2021 will be automatically adjusted to reflect the new $40.00 administration fee. Providers will not have to take any further action.

III. Medicaid Managed Care

A. MMC Coverage Policy

The Medicaid coverage policy in Section I above applies to all types of MMC Plans.

B. MMC Reimbursement

The COVID-19 vaccine administration fees and billing instructions in Section II above are specific to Medicaid FFS. For individuals enrolled in MMC, providers should check with the individual´s MMC Plan for implementation details, reimbursement fees and billing instructions.

  1. Effective April 1, 2021, MMC Plans will reimburse providers no less than the Medicaid FFS rate for COVID-19 vaccine administration.
  2. MMC Plans must cover the cost of vaccine administration by qualified providers who do not participate in the MMC Plan´s network.
  3. Rate-based and office-based provider reimbursement for the vaccine administration must be made separately from visit reimbursement, as detailed in Section II.

Additional Resources:

Questions:

  • Medicaid FFS coverage and policy questions should be directed to the Office of Health Insurance Programs, Division of Program Development and Management, at (518) 473-2160 or FFSMedicaidPolicy@health.ny.gov.
  • MMC reimbursement, billing, and/or documentation requirement questions should be directed to the enrollee´s MMC plan.
  • Medicaid FFS claim questions should be directed to the eMedNY Call Center at (800) 343-9000.
  • Medicaid FFS Pharmacy Policy questions should be directed to (518) 486-3209 or ppno@health.ny.gov.