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Which federal programs paid hospitals for COVID-19 treatment and how were payment rates calculated?

Checked on November 20, 2025
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Executive summary

Federal programs that paid hospitals for COVID-19 care included the Provider Relief Fund (PRF) — a $178 billion HHS program to compensate providers for COVID-related expenses and lost revenue — and Medicare adjustments such as the Inpatient Prospective Payment System (IPPS) add-ons like the New COVID-19 Treatments Add-on Payment (NCTAP) and other temporary pandemic-era payment flexibilities [1] [2]. Details about exact payment formulas and all programs are only partly covered in these documents: PRF terms and balance‑billing rules are in an HHS OIG audit and Congress’s appropriation is cited there, while CMS rulemaking documents discuss Medicare add‑ons and temporary payment policies [1] [2].

1. Provider Relief Fund: large, lump‑sum federal support with conditions

Congress appropriated $178 billion to HHS for the Provider Relief Fund (PRF) to reimburse eligible providers for health care expenses or lost revenue attributable to COVID‑19; HHS issued PRF payments with terms and conditions, including a balance‑billing prohibition for insured patients treated by out‑of‑network providers that received PRF funds [1]. The Office of Inspector General’s audit found many hospitals were uncertain how to comply with HRSA guidance and that lack of early, detailed guidance may have led to improper patient billing totaling $637,035 among selected cases — signaling that PRF was a blunt but large instrument with compliance complexity [1].

2. Medicare inpatient payments and COVID‑specific add‑ons

CMS used existing Medicare payment systems to alter hospital incentives during the pandemic. For example, CMS established the New COVID‑19 Treatments Add‑on Payment (NCTAP) under the IPPS to increase IPPS payment amounts for qualifying COVID‑19 cases and to reduce disincentives for hospitals adopting new COVID treatments [2]. CMS has since adjusted availability of such add‑ons in subsequent rulemaking — including reiterations that some COVID‑related add‑ins would not be available for certain fiscal years — indicating these were temporary, policy‑driven rate changes rather than permanent rate restructurings [2] [3].

3. How Medicare payment rates were calculated or adjusted (what sources show)

CMS’s approach relied on existing prospective payment systems and targeted add‑on payments: IPPS base payments continued to use DRG‑based prospective rates while NCTAP provided additional per‑case payments for eligible cases to cover costs of new COVID‑19 treatments [2]. CMS rulemaking and fact sheets referenced using hospital data and statutory authorities to set relative rates and add‑on amounts, and later IPPS rules clarified eligibility windows and availability for such add‑ons [2] [3]. Available sources do not provide the detailed arithmetic formulas or all calibration inputs used to compute each add‑on dollar amount in these excerpts.

4. Telehealth and outpatient payment flexibilities tied to the PHE

During the public health emergency, CMS expanded telehealth reimbursement and other payment flexibilities (for example, allowing audio‑only services and permitting patients’ homes as originating sites), and some of these payment methods were reimbursed under standard Medicare rates or temporary methodologies through 2025 [4] [5] [6]. These changes affected hospital and outpatient revenue streams by broadening what services were billable and by aligning some telehealth reimbursement with existing prospective payment or PFS frameworks [4] [5].

5. What the sources don’t say (important gaps and limits)

The provided materials document high‑level program existence, authorizations, and policy intent — PRF appropriations, PRF terms and balance‑billing, establishment of NCTAP, and telehealth payment flexibilities — but they do not include the full payment schedules, line‑by‑line formulas, or the complete list of every federal program and procurement that flowed payments to hospitals for COVID care [1] [2] [5]. For instance, precise per‑case dollar amounts for PRF disbursements, detailed NCTAP calculation steps, and any confidential HHS allocation methodologies are not contained in the snippets provided [1] [2].

6. Competing perspectives and implicit agendas

HHS/OIG’s audit frames PRF compliance as a governance problem — hospitals were uncertain and HRSA guidance may have been insufficient, implying a need for clearer rulemaking and oversight [1]. CMS rule documents emphasize policy flexibility to sustain access and encourage adoption of new treatments [2]. These are different institutional viewpoints: oversight bodies highlight compliance and accountability, while CMS highlights program design to maintain care delivery and incentivize treatment adoption, meaning debates over the balance of speed, flexibility, and oversight are implicit in the sources [1] [2].

7. Bottom line for readers

Federal COVID hospital support combined large, discretionary grants (PRF) with targeted Medicare payment adjustments and temporary telehealth and outpatient reimbursement changes; details on precise rate‑setting calculations are partially described in CMS rulemaking and oversight reports but complete formulas and all program lists are not present in the sourced excerpts [1] [2] [5]. For a full technical accounting of every payment rate and allocation method, consult the complete HRSA/PRF guidance, CMS IPPS/NCTAP final rules, and related Federal Register entries beyond the materials cited here [1] [2].

Want to dive deeper?
Which specific federal funds (e.g., Medicare, Medicaid, CARES Act, Provider Relief Fund) reimbursed hospitals for COVID-19 care?
How did Medicare reimbursement rules change for COVID-19 hospital stays, ICU care, and telehealth during the pandemic?
What methodology determined payment rates under the Provider Relief Fund and CARES Act for uncompensated COVID-19 expenses?
How did private insurance and state Medicaid programs coordinate with federal COVID-19 hospital payment policies?
Were hospitals paid differently for COVID-19 patients in emergency use settings, clinical trials, or for using remdesivir and other therapies?