COVID-19 Guidance for Medicaid Providers

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

As of 6/17/20
Updates are highlighted

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

Per the Governor´s Executive Order #202.24, during the declared disaster emergency, Section 6801 of the NYS Education Law and Subdivision (6) of section 571 of the NYS Public Health Law have been temporarily modified to the extent necessary to authorize 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, in patients suspected of a COVID-19 infection, or suspected of having recovered from COVID-19 infection, subject to completion of appropriate training developed by the Department of Health; and,
  • ✓ be designated as a qualified healthcare professional for the purpose of directing a limited service laboratory, pursuant to subdivision 579(3) of the Public Health Law, to test patients suspected of a COVID-19 infection or its antibodies provided that such test is FDA-approved and waived for use in a limited service laboratory.

This guidance is effective May 22,2020 and shall remain in effect for the remainder of the disaster emergency declared by Executive Order No. 202.24, or until the issuance of subsequent guidance by the NYSDOH prior to the expiration of such state disaster emergency declaration.

NYS Medicaid FFS will cover COVID-19 specimen collection or CLIA waived COVID-19 testing at pharmacies in accordance with this Executive Order. 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) (see billing instructions below). Dual eligible members will continue to access testing services through Medicare.

FFS Pharmacy Billing Instructions:

Table 1 - Billing Instructions for Lab Specimen Collection or CLIA waived COVID-19 testing
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) Enter Pharmacist National Provider Identifier (NPI) number*

* At this time, claims submitted with the Supervising Pharmacist´s NPI, in the Prescriber ID field (411-DB), will deny with edits 00898 (prescribing provider category of service invalid for pharmacy) and 01237 (prescriber license not on NYS license file).  The NCPDP response will show code “25”- M/I Prescriber ID. DOH is working on system changes that will prevent these denials. Until these changes are implemented, claims may be submitted using a non-Supervising pharmacist´s NPI in that field.  Updated guidance will be issued once this has been resolved. 

Please see the July 2016 Medicaid Update for further guidance on origin code and serial number values.

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

*Pharmacies that are performing and billing for COVID-19 testing should not bill for specimen collection. Reimbursement for 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 for COVID-19 testing should not bill Medicaid in addition. Information regarding tests that have been granted FDA Emergency Use Authorization can be found here.

Services must be provided and documented in accordance with the guidance issued by the NYS Department of Health.

Medicaid Managed Care (MMC) Billing

MMC plans will be providing separate guidance to pharmacies, which will allow billing for service dates on or after the effective date of this guidance. Pharmacies participating in MMC should check with the individual health plans to determine how each MMC plan will apply this FFS policy and when their billing policies for COVID-19 laboratory testing at pharmacies will be established.

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

For Medicaid FFS Pharmacy Policy questions, please contact