HHS Says States Must Honor Religious Vaccine Exemptions or Risk Losing Federal Funds

Department letter admits vaccines fall under federal conscience statutes—putting state mandates in direct conflict with religious freedom laws.

This article originally appeared on Jon Fleetwood’s Substack and was republished with permission.

Guest post by Jon Fleetwood

Under Secretary Robert F. Kennedy Jr.’s leadership, the U.S. Department of Health and Human Services (HHS) has just confirmed in writing what vaccine safety advocates have long argued: federal law requires states to honor religious vaccine exemptions.

And the stakes couldn’t be higher.

West Virginia alone risks $1.37 billion in Medicaid funding if it refuses to comply.

The move comes after Secretary Kennedy expelled the American Academy of Pediatrics and allied groups from HHS advisory roles, following those groups’ push to eliminate personal belief vaccine exemptions.

Taken together, Kennedy is carving out a clear pattern of dismantling the influence of pro-mandate lobbies while reinforcing legal protections for conscience and religious freedom in vaccine policy.

Federal Civil Rights & Conscience Protections Apply to Vaccines

The letter, sent August 21, 2025, from HHS’s Office for Civil Rights (OCR) to West Virginia health officials, makes clear that vaccines fall under the umbrella of conscience protections.

As the agency put it:

“OCR enforces 26 conscience statutes applicable to various funding streams as well as 21 religious non-discrimination provisions in other federal statutes and regulations, which include a number of grant and block grant programs… These protections are applicable to specific health programs and cover a range of topics depending on the statute, including abortion, sterilization, assisted suicide, advanced directives, vaccines, and compulsory health services.”

In other words, HHS is directly acknowledging that vaccines are covered under federal conscience statutes, meaning religious and moral objections cannot simply be brushed aside by state laws or health agencies.

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The Vaccines for Children Program Requires Respect for Exemptions

The letter highlights the federal Vaccines for Children Program (VCP), which provides pediatric vaccines to children who are uninsured or Medicaid-eligible.

Importantly, Congress built into the law an explicit protection for state-level exemptions:

“Providers participating in the VCP must comply ‘with applicable State law, including any such law relating to any religious or other exemption.’”

Here, HHS is saying plainly that the VCP does not override exemptions—it enforces them.

This means states cannot participate in the program, or keep federal dollars flowing, while ignoring their own exemption laws.

West Virginia’s Religious Freedom Law Now Overrides Its Vaccine Mandate

West Virginia’s 2015 compulsory vaccination law allows only medical exemptions, but that changed when lawmakers passed the Equal Protection for Religion Act (EPRA) in 2023.

The letter underscores how EPRA rewrote the legal landscape:

“Notwithstanding any other provision of law, no state action may: (1) Substantially burden a person’s exercise of religion unless… essential to further a compelling governmental interest; and is the least restrictive means of furthering that compelling governmental interest; nor (2) Treat religious conduct more restrictively than any conduct of reasonably comparable risk.”

Translated: the state can’t force vaccines on religious objectors unless it proves it has no other choice, and even then, it must use the least restrictive approach.

Governor Morrisey and State Courts Already Back Exemptions

HHS noted that West Virginia Governor Patrick Morrisey already issued Executive Order 7-25 earlier this year, directing state health officials to create a religious exemption process for schoolchildren.

The letter states:

“On January 14, 2025, West Virginia Governor Patrick Morrisey issued Executive Order 7-25, directing West Virginia’s Commissioner of the Bureau for Public Health and the State Health Officer to establish an exemption process for those who want to send their children to public school, and who have religious or moral objections to receipt of one or more vaccines otherwise required by the State’s compulsory immunization law.”

HHS went further, pointing out that Morrisey’s interpretation was “recently affirmed” by Judge Froble of the Circuit Court of Raleigh County.

In short, both the state executive and judiciary have already confirmed what HHS is now echoing: religious exemptions must be recognized.

$1.37 Billion in Federal Funds on the Line

The letter warns that because West Virginia participates in the Vaccines for Children Program and receives massive federal Medicaid funding, it is obligated to enforce EPRA’s religious exemption provisions:

“West Virginia is a participant in the VCP and receives $1.37 billion from the Centers for Medicare & Medicaid Services each year as the federal Medicaid contribution. Therefore, West Virginia is obligated to ensure that its VCP providers comply with applicable state laws like EPRA, which requires recognition of religious exemptions from West Virginia’s Compulsory Vaccination Law.”

That means this is no longer an academic debate.

If the state fails to recognize exemptions, it risks losing over a billion dollars in federal funding—a direct financial penalty tied to conscience protections.

Federal Priority: Conscience & Religious Freedom

Finally, HHS emphasizes its enforcement role and says it stands ready to receive complaints if West Virginia or any other state resists:

“It is a priority of the Department to enforce these laws and help health care entities and health care providers understand these laws. OCR is available to provide technical assistance related to conscience protections, or receive complaints related to conscience.”

This is not a suggestion—it is a declaration that HHS will intervene if states or providers refuse to comply.

Bottom Line

This letter marks a watershed moment.

For decades, states like West Virginia justified banning religious exemptions by hiding behind compulsory vaccination laws.

But HHS just made it clear: federal law, backed by federal funding, requires those exemptions to be honored.

Other states with similar hardline policies—such as California and New York—may now face pressure under the same logic.

Federal conscience protections don’t stop at the Appalachians.

Copyright 2025 Jon Fleetwood

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