The Biden administration’s requirement that church leaders decide who gets a religious exemption to COVID-19 vaccine mandates has created a crisis of conscience for Catholics, dividing their bishops and sparking outcry among some First Amendment scholars.

In recent weeks, various U.S. bishops have taken positions at odds with each other on granting the exemptions, dividing their flocks bitterly and suggesting that the faithful might simply hop jurisdictions to get a dispensation.

The bishops of Philadelphia, Chicago, San Diego, and New York City have all forbidden their priests from granting religious exemptions to churchgoers who ask for them. But others, including all four Catholic bishops in Colorado, have issued statements praising the government’s allowance for exemptions and encouraging their pastors to consider all requests.

In the midst of the resulting infighting that has erupted among Catholics about whether to vaccinate, some First Amendment legal scholars have blamed the nation’s second Catholic president for tormenting his coreligionists by taking away their sense of moral autonomy in the matter.

“The U.S. Supreme Court has made clear that the First Amendment forbids the government from attacking an individual’s religious belief just because it may not conform to the dictates of a particular church or its leaders,” said Peter Breen, vice president and senior counsel at the Thomas More Society, a Chicago-based religious freedom advocacy group.

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“The government has no authority to wade into doctrinal disputes, and from a First Amendment perspective, once it is clear that a person’s religious belief is ‘sincere,’ that part of the inquiry ends.”

Breen, a former Illinois state representative for the 48th district from 2015 to 2019, said the Supreme Court established in the 1989 case Frazee v. Illinois Department of Employment Security that a worker could not be denied unemployment for refusing to work on Sunday for religious reasons, providing a precedent to challenge Biden’s policy.

He added that Biden’s policy of requiring Catholics to get “a note from the pastor” to avoid vaccine mandates seemed hostile to the spirit of the First Amendment of the U.S. Constitution, a “first freedom” that protects the free exercise of believers’ consciences even from their own religious leaders.

Kathryn Jean Lopez, the editor-at-large of National Review Online and a Catholic author, said bishops forbidding religious exemptions have caused particular pain to a female acquaintance who had an abortion and “feels it would be an insult to God to turn around and benefit from another child’s death.”

“This does seem to be another way we are chipping away at conscience rights in the United States,” Lopez said of Biden’s policy. “We can both encourage people to get a vaccine and respect the rights of individuals to exercise their freedom to act in accord with their conscience.”

For many Catholics, the objection to the vaccines arises from researchers using fetal stem cells in their testing and production, violating church teaching on abortion by creating and destroying human life for laboratory purposes.

“Even accepting what our church has said about moral culpability, there are people of goodwill who are agonizing over the coercion to get the vaccines — good people worried about the trajectory of a country that is expanding and not restricting the use of aborted babies in medical research,” Lopez said.

Church leaders have declared the Moderna and Pfizer vaccines less objectionable than the Johnson & Johnson vaccine because the former used stem cells only in testing, whereas the latter used them in both testing and production. Church leaders have also said the latter is morally acceptable if no others are available.

The United States Conference of Catholic Bishops and the Vatican have encouraged Catholics to get vaccinated, with Pope Francis even participating in a recent public-service announcement promoting the vaccines.

But last December, the Vatican’s Congregation for the Doctrine of the Faith ruled with the approval of Pope Francis that vaccination against COVID-19 is not a moral obligation.

“At the same time, practical reason makes evident that vaccination is not, as a rule, a moral obligation and that, therefore, it must be voluntary,” the Congregation for the Doctrine of the Faith said in its “Note on the morality of using some anti-Covid-19 vaccines.”

This past January, the U.S. Conference of Catholic Bishops affirmed the same in its “Answers to Key Ethical Questions About COVID-19 Vaccines.”

Ronald J. Rychlak, a longtime associate dean of the School of Law at Ole Miss and a Catholic historian of Pope Pius XII, said religious exemptions for vaccines should work on the same principle of individual autonomy as conscientious objection did during World War II when soldiers on various sides made up their own minds about whether it was just to fight.

“If the church says vaccines are acceptable to the faith, I have some questions from the church’s perspective about an individual’s ability to claim it, but I guess it should follow the same approach,” Rychlak said.

Sean Salai writes about politics and religion in Washington, D.C. He’s a pastoral theologian with a Doctor of Ministry in digital evangelization from the Catholic University of America in Washington, D.C., and is the author of several Catholic books.