Coding Guidance for Pharmacies


COVID-19 Sample Collection and Testing Claims Submission

Effective: August 21, 2020


In response to the current novel Coronavirus (COVID-19) emergency situation, and pursuant to the New York State Medicaid Fee-for- Service Policy and Billing Guidance for COVID-19 Testing and Specimen Collection at Pharmacies, New York Medicaid plans will reimburse Providers for COVID-19 specimen collection or CLIA waived COVID-19 testing for Medicaid Members, when such collection or testing is in compliance with the Governor’s Executive Order #202.24. 


The terms and rates herein are subject to change pursuant to any changes or updated to the New York State Medicaid Fee-for- Service Policy and Billing Guidance for COVID-19 Testing and Specimen Collection.

NCPDP D.0. Claim Segment Field


436-E1 (Product/Service ID Qualifier) Enter a value of 03.
407-D7 (Product/Service ID) Enter the 11-digit NDC for test kit, if there is no test kit enter valid NDC for specimen collection
440-E5 (Professional Service Code)

Enter a value of MA

411-DB (Prescriber ID)

Enter the Pharmacist National Provider Identifier (NPI) number.


Reimbursement for Lab Specimen Collection or CLIA waived COVID-19 Testing*

Description Reimbursement
Specimen collection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]) (NDC 99999-0992-11 only) $23.46
*2019-nCoV Coronavirus, SARS-CoV-2/2019-nCov (COVID-19), any technique, multiple types or subtypes (includes all targets), non-CDC


*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 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.


Only test kits with an FDA approved Emergency Use Authorization (EUA) are covered.  Specimen collection without a test kit is also covered.  To identify FDA approved tests,see the Test Kit Manufacturers and Commercial Laboratories Table


Subject to change, the following are sample NDCs covered under this program:

NDC 11877-0011-26       ID NOW COVID-19 TEST KIT

NDC 22066-0005-11       RAPID RESPONSE COVID-19 TEST

NDC 60004-0417-80       COVID-19 Test Administration

NDC 99999-0992-11       SPECIMEN COLLECTION

NDC 00042-0222-24       COVID-19 TEST SPECIMEN COLLECT



Please be aware that the Medicaid program prohibits providers from billing members for charges for COVID-19 protective measures including personal protective equipment (PPE). Please ensure that only the copay returned in the NCPDP response field is collected from a Medicaid member, and no additional charges are added for PPE. 

Our Call Center is currently experiencing extremely high volume and longer wait times. For questions related to COVID-19, visit our COVID-19 FAQs