New York State (NYS) Medicaid Fee-for-Service (FFS) Policy and Billing Guidance for COVID-19, Testing and Specimen Collection at Pharmacies

As of 12/16/2021
Updates are highlighted

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

The following guidance shall continue to remain in effect in accordance with the Public Readiness and Emergency Preparedness Act (PREP Act) for licensed pharmacists to:

  • order COVID-19 tests, approved by the Food and Drug Administration (FDA), to detect SARS-CoV-2; or its antibodies;
  • administer COVID-19, tests subject to CLIA Certificate of Waiver requirements pursuant to the federal clinical laboratory improvement act of nineteen hundred eighty-eight.

NYS Medicaid FFS will cover COVID-19 specimen collection or CLIA waived COVID-19 testing at pharmacies in accordance with the PREP Act, with no member cost sharing. Pharmacies will only be able to bill for Medicaid non-dual eligible members for FDA approved or cleared tests or tests that have been authorized by the FDA under Emergency Use Authorization (EUA) and in agreement with the level of complexity assigned by Wadsworth Lab. Complexity levels are available here. See billing instructions below. Dual eligible members will continue to access testing services through Medicare.

Effective December 13th, 2021, NYS Medicaid FFS will cover COVID-19 diagnostic tests with "at home" sample collection for reimbursement with no member cost sharing. Policy and billing guidance can be found here: NYS Medicaid Pharmacy Policy and Billing Guidance for At Home COVID-19 Testing Coverage

FFS Pharmacy Billing Instructions for COVID-19 Testing and Specimen Collection:
  • Services must be provided and documented in accordance with the guidance issued by NYSDOH.
Table 1 - Billing Instructions for Lab Specimen Collection or CLIA waived COVID-19
NCPDP D.0. Claim Segment Field Value
436-E1 (Product/Service ID Qualifier) Enter a value of "09" (HCPCS), which qualifies the code
407-D7 (Product/Service ID) Enter one applicable procedure code from Table 2
444-E9 (Pharmacist ID) Enter Pharmacist National Provider Identifier (NPI) number
411-DB (Prescriber ID) Please leave field *
461-EU (Prior Authorization Type Code) Enter 04= Exempt Copay * *

* Effective August 6, 2020, claims should be submitted with blanks in the Prescriber ID (411-DB).
**NCPDP D.0 Companion guide can be found here.

Please see the July 2020 Medicaid Update for further guidance on origin code and serial number values that must be submitted on the claim. In the origin code field use “5” and the corresponding serial number of “99999999” for “Pharmacy dispensing” when applicable for non-patient  specific orders.

Table 2 - Code List and Reimbursement for Lab Specimen Collection or CLIA waived COVID-19 testing
Code Description Reimbursement
G2023 Specimen collection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]) $23.46
U0002* 2019-nCoV Coronavirus, SARS-CoV-2/2019-nCov (COVID-19), any technique, multiple types or subtypes (includes all targets), non-CDC $51.31
87635* Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), amplified probe technique. $51.31
87426* (effective 06/25/2020) Infectious agent antigen detection by immunoassay technique, (e.g., enzyme immunoassay [EIA], enzyme-linked immunosorbent assay [ELISA], immunochemiluminometric assay [IMCA]) qualitative or semiquantitative, multiple-step method; severe acute respiratory syndrome coronavirus (e.g., SARS- CoV-2, SARS-CoV-2 [COVID-19]). $45.28
87811* (effective 01/01/2021) Infectious agent antigen detection by immunoassay with direct optical (i.e., visual) observation; severe acute respiratory coronavirus 2 (SARS-CoV-2) (coronavirus disease [COVID-19]). $41.38

*Pharmacies that are perf orming and billing for COVID-19 testing should not bill for specimen collection. Reimbursement or the test includes specimen collection and generating the lab report. Furthermore, pharmacies who are already being provided payment, from another source, for either lab specimen collection or f or COVID-19 testing should not bill Medicaid in addition. Inf ormation regarding tests that have been granted FDA Emergency Use Authorization can be found here.

Medicaid Managed Care (MMC)Billing

Individual MMC plan billing guidance for COVID-19 laboratory testing and specimen collection for pharmacies, is posted on the Medicaid Managed Care Pharmacy Benefit Information Center. Providers can select the MMC plan in question and then select the COVID Testing-Pharmacy Billing Guidance hyperlink to get the plan specific guidance page on their website. Providers can also access this information on the individual MMC plan websites. For MMC billing questions unanswered by using these resources, please contact the individual plan using the information in the link above.

For Medicaid FFS billing questions, please contact the eMedNY Call Center at (800) 343-9000.

For Medicaid FFS Pharmacy Policy questions, please contact