COVID-19 Vaccine Information for Providers

COVID-19 Vaccine Information for Providers


New York State requires active involvement of its health care providers to roll out the COVID-19 vaccine to its 20 million residents. Health care providers must stay up-to-date on the COVID-19 vaccine distribution and implementation. 

How To Order the COVID-19 Vaccine

Step One - Register for the Immunization Information System:

Healthcare providers are strongly recommended to register in NYSIIS for providers in NYS, outside of NYC, and with CIR for providers located in NYC. This is because all COVID-19 Vaccination Program providers (each location submitting a profile) will need a NYSIIS account (for providers outside of NYC) or CIR account (for providers located in NYC). Your organization may currently have a NYSIIS or CIR account, but it is important to ensure that the appropriate staff have access.

Step Two – Enroll in the COVID-19 Vaccination Program:

  • In addition to registering with NYSIIS or CIR, providers must enroll in the COVID-19 Vaccination Program. NYSDOH and NYC DOHMH are implementing a phased approach to provider enrollment and will notify healthcare facilities, providers and professional groups as each new group is opened for enrollment.
  • Providers in NYS, outside of NYC, will enroll in the NYS COVID-19 Vaccination Program through the Health Commerce System application "COVID-19 Vaccine Program Provider Enrollment"  and should review the NYSDOH COVID-19 Vaccination Program Enrollment Letter for guidance.  Providers in NYC will enroll in the NYC COVID-19 Vaccination Program through the CIR.
  • Networks with facilities or providers in both NYS and NYC should enroll their facilities or providers outside of NYC in the NYS COVID-19 Vaccination Program through the Health Commerce System and enroll their facilities or providers in NYC in the NYC Covid-19 Vaccination Program through the CIR.

Step Three – Ordering, Receiving and Administering Vaccine

  • When COVID-19 vaccine is available, providers will order COVID-19 vaccine through NYSIIS (for providers in NYS, outside of NYC) and CIR (for providers in NYC). Orders will be reviewed and approved by NYS DOH and shipped directly from the vaccine manufacturer or CDC distributor.
  • When vaccine is available, providers will monitor vaccine inventory; enter doses administered and/or perform data exchange (uploading and downloading data) between the provider's electronic health system and NYSIIS/CIR; enter vaccine returns and wastage; and generate reports for internal review (e.g. doses administered) in NYSIIS/CIR.

For questions, call the NYSDOH COVID-19 hotline 1-888-364-3065. Health care providers interested in learning more about the COVID-19 Vaccine Program may contact the NYSDOH at [email protected]. NYC providers with enrollment questions may contact NYC DOHMH at [email protected] or COVID-19: Vaccines.


Prioritization Guidance

Operational Guidance

Providers can find a range of documents and guidance on administering the COVID-19 vaccine. 


    Guidance for The New York State COVID-19 Vaccination Program

    On September 24, 2021, under the US Food and Drug Administration (FDA) amended emergency use authorization (EUA) for the Pfizer-BioNTech COVID-19 Vaccine, the CDC issued recommendations for a single booster dose for individuals 65 years of age or older, as well as long-term care facility residents; individuals age 50-64 with underlying medical conditions; individuals age 18-49 with underlying medical conditions, based on individual benefit and risk; and individuals age 18-64 who are at an increased risk for COVID-19 exposure or transmission because of occupational or institutional setting. Underlying conditions and occupational settings are enumerated below.




    Requirements Regarding NYSIIS and CIR

    The following document provides guidance to remind all authorized vaccine administrators concerning requirements reragring the New York State Immunization Information System (NYSIIS) and City Immunization Registry (CIR). 




    Regional Vaccination Network Letter

    This letter provides additional detail on the establishment of Regional Vaccination Networks and clarifies the role of health care providers in this effort and emphasizes the expectation that health care providers fully participate in their local Regional Vaccination Network.



Provider Training