COVID-19 Vaccine Administration: Preparing to Electronically Submit Pharmacy Claims

Originally published December 28, 2020
Updated on April 26, 2021
Most recent updates are denoted with two plus signs (++)

Current Guidance

++This is the third article in the COVID-19 Vaccine Administration series and originally covered how pharmacy providers should plan to submit their claims in the coming weeks. As of the original publication of this article, pharmacy providers were instructed to continue to hold on submitting their claims to Medi-Cal. Providers have been notified in a subsequent News article that Medi-Cal is ready to intake claims for the COVID-19 vaccine administration. Medi-Cal can now intake and process administration of currently approved COVID-19 vaccines on all pharmacy claim submission types.

++As previously announced, with the recent federal approval of COVID-19 vaccines, the Department of Health Care Services (DHCS) is seeking federal approval to help support delivery of the vaccine to all Medi-Cal beneficiaries. DHCS will follow California’s COVID-19 vaccination plan, which was approved by the California Department of Public Health (CDPH). In order to receive and administer COVID-19 vaccines, all California healthcare providers should refer to the enrollment instructions on the CDPH website, email the California COVID-19 Vaccination Program at or call the COVID-19 Call Center at (833) 502-1245, Monday through Friday, from 9 a.m. to 5 p.m. More information is also available on the COVID-19 Vaccine Questions and Answers web page.

Additionally, Pharmacy providers are encouraged to administer the vaccine in accordance with the most recent CDPH Allocation Guidelines for COVID-19 Vaccine.

++Because the federal government will pay for the initial vaccines, there is no Medi-Cal provider reimbursement for the COVID-19 vaccine itself. DHCS plans to reimburse the associated COVID-19 vaccine administration fee at the Medicare allowable rate for all claim types, including pharmacy, based on the number of required doses. As of the original publication of this article, DHCS has requested federal approval to provide coverage of vaccine administration for Medi-Cal beneficiaries who have restricted scope coverage or who are enrolled in the Family Planning, Access, Care, and Treatment (Family PACT) program, as well as the COVID-19 Uninsured Group program. In addition, DHCS has submitted a State Plan Amendment to request approval from the Centers for Medicare and Medicaid Services (CMS) to reimburse Federally Qualified Health Centers (FQHCs), Rural Health Clinics (RHCs), and Indian Health Services-Memorandum of Agreement (IHS-MOA) 638 clinics a fee-for-service rate for vaccine administration when the encounter does not meet all of the requirements of a billable visit (i.e. vaccine-only administration). For additional updates regarding these requests for federal approvals, providers should refer to the latest guidance on the COVID-19 Medi-Cal Response page.

Pharmacy providers should note that they will not be reimbursed for the vaccine cost or a dispensing fee for a federally-provided vaccine.

Claim submission for pharmacy providers will be allowed in three phases:

  • Phase One: Real-time electronic submission via NCPDP Standard D.0.

  • Phase Two: Real-time electronic submission via Real Time Internet Pharmacy (RTIP)

  • Phase Three: Electronic batch submission (NCPDP 1.2) or hard copy submission of the Pharmacy Claim Form (30-1)

++Instructions on how to submit real-time electronic claims (NCPDP Standard D.0) were originally included in this article. Instructions on how to properly bill using RTIP, batch electronic formats (NCPDP 1.2) and hard copy submission using the Pharmacy Claim Form (30-1), are now available as well.

++All other pharmacy policy billing requirements remain in effect. As of January 19, 2021, all pharmacy claim submission types can be submitted to Medi-Cal:

++For the most current direction regarding whether or not claims should be submitted, and what behavior to expect when submitting, providers should refer to the "Pharmacy Claim Submissions” and “Medical and Outpatient Claim Submissions” tables on the COVID-19 Medi-Cal Response page.

Preparing to Submit Real-Time Transactions

++Currently the U. S. Food and Drug Administration (FDA) has provided Emergency Use Authorization (EUA) for the following vaccine manufacturers. In the original publication of this article, billing instructions were included in this article, but in order to support flexibility as additional COVID-19 vaccines are approved and administration guidance evolves, the policy has been moved to vaccine-specific pages:

As other vaccine manufacturers are approved by the FDA, additional billing instructions will be issued and added as links.

Upcoming Updates

Updates regarding the administration of the COVID-19 vaccine will be shared as they are made available. An FAQ regarding the administration of the COVID-19 vaccines is available on the DHCS website. The FAQ is updated as needed.

This guidance is only effective for COVID-19 vaccines purchased by the federal government. At a future date, DHCS will provide an end date to this temporary policy and instruct providers on how they should bill for the reimbursement of provider purchased COVID-19 vaccines.

Providers with questions should contact the Telephone Service Center (TSC) Help Desk at 1-800-541-5555, 8 a.m. to 5 p.m., Monday through Friday, except holidays. Border providers and Out-of-State billers billing for in-state providers, should call 1-916-636-1200.