A new MLN Matters Article MM11882 on Influenza Vaccine Payment Allowances – Annual Update for 2020-2021 Season is available. Learn about payment allowances, effective August 1. The Medicare Part B payment allowance limits for influenza and pneumococcal vaccines are 95 percent of the average wholesale price (AWP), except where the vaccine is provided in a hospital outpatient department, Federally Qualified Health Center (FQHC) or Rural Health Clinic (RHC). Payment for vaccine provided in these specific settings is based on reasonable cost. Annual Part B deductible and coinsurance amounts do not apply.