COVID-19 Vaccine Information for Providers –

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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. 

Ordering 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.

  • For health care providers located in NYS outside of NYC, take the following steps for new users in NYSIIS – see the Checklist to Go Live with NYSIIS: 1). NYSIIS is located on the Health Commerce System (HCS). If responsible staff do not yet have an HCS account, they must apply for one, 2). Take the NYSIIS Administrative User Training.
  • For health care providers located in NYC, go to the online CIR registration page.

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.


  • Ordering COVID-19 Vaccine in NYSIIS

    Updated June 28, 2022 – Providers (outside of NYC) enrolled in the NYSDOH COVID-19 Vaccination Program can place COVID-19 Vaccine orders in NYSIIS, via the Manage Orders module.

Operational Guidance

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

  • New York State COVID-19 Vaccine Program Guidance for Vaccine Transport

    Updated March 29, 2022 – Routine transport of vaccine is not recommended. Each transport increases the risk of exposing vaccine to inappropriate storage conditions, which compromises the viability of vaccines. However, in certain situations transporting vaccine may be necessary. Opened vials cannot be transported.

  • Reporting Vaccine Wastage

    February 7, 2022 – When COVID-19 vaccine doses are unused, spoiled, damaged, or expired they are considered vaccine wastage.

  • COVID-19 Policy for Predrawn Vaccine

    May 3, 2021 – Although standards for vaccine administration typically do not include predrawing (also known as “prefilling”) of syringes due to concerns over compromising or wasting vaccine, the Centers for Disease Control and Prevention (CDC) has permitted predrawing for COVID-19 vaccines, subject to certain qualifications.

  • Vaccination Program Enrollment Letter

    February 12, 2021 – Please review the information in this letter and each of the referenced resource documents (links provided) and complete the enrollment application in the HCS online application tool.

  • Guidance on Moderna Extra Dose

    December 23, 2020 – Guidance for vaccine providers who may be able to withdraw more than 10 doses from a single 10-dose vial.

  • Regional Vaccination Network Letter

    December 18, 2020 – 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.

  • Pharmacists Administering the COVID-19 Vaccine

    December 15, 2020 – This certification permits licensed physicians and certified nurse practitioners to issue a non-patient specific order to pharmacists for the administration of COVID-19 vaccine.

  • Requirements Regarding NYSIIS and CIR

    December 13, 2020 – Guidance to remind all authorized vaccine administrators concerning requirements regaridng the New York State Immunization Information System (NYSIIS) and City Immunization Registry (CIR). 

Provider Training