President Trump told religious leaders Thursday that he wants to “destroy” a longstanding IRS rule that bars churches from endorsing political candidates, while progressive groups raised alarms that he’ll expand legal protections for people opposed to same-sex marriage or contraceptive coverage on religious grounds.

Speaking at the annual National Prayer Breakfast in Washington, Mr. Trump said he plans to eliminate the so-called Johnson amendment as part of a broader effort to restore religious freedom protections to individuals, businesses and faith leaders.

“I will get rid of and totally destroy the Johnson amendment and allow our representatives of faith to speak freely and without fear of retribution,” Mr. Trump said.

The 1954 IRS provision prevents tax-exempt organizations from campaigning for or endorsing political candidates. Some Republican lawmakers want to repeal it, and Mr. Trump had promised during his campaign to get rid of the measure.

The president did not elaborate on how he intends to carry out the proposed move. But two House Republican lawmakers and Sen. James Lankford, Oklahoma Republican, introduced legislation Wednesday that would amend the tax code to “restore free speech” for churches and nonprofits as long as the speech takes place “in the ordinary course” of the organization’s activities, and related expenses are minimal.

“For too long the IRS has used the Johnson amendment to silence and threaten religious institutions and charitable entities,” said Rep. Jody B. Hice, Georgia Republican. “As a minister who has experienced intimidation from the IRS firsthand, I know just how important it is to ensure that our churches and nonprofit organizations are allowed the same fundamental rights as every citizen of this great nation.”

Some religious groups objected to the proposal. Rabbi Jack Moline, president of the Interfaith Alliance, said repealing the Johnson amendment “would undermine religious freedom by plunging houses of worship into partisan politics and inviting the rewards and punishments of patronage.”

“We strongly urge Congress to oppose the effort to undermine the Johnson amendment, which has nothing to do with religious freedom and everything to do with grabbing power for the Religious Right,” the rabbi said.

White House press secretary Sean Spicer said the administration seeks to strike a balance when defending religious liberty, dismissing a purported draft executive order that would vastly expand protections for businesses and institutions opposed to same-sex marriage or providing contraception coverage.

Mr. Spicer said that the president recognizes “there is a line” that must be respected between religious liberty and tolerance in the workplace. Mr. Trump wants to make sure the “line is less blurry,” he said.

“We shouldn’t impose a religion on anybody. We are free to express our religion or not have one. That in our country is an equally valid way of living your life,” Mr. Spicer told reporters at the White House. “At the same time, people who want to express their faith shouldn’t be ostracized because they want to do that.”

The president’s comments at the prayer breakfast helped fuel concerns among liberal groups that Mr. Trump plans to undermine protections against discrimination against gays, as well as allow businesses to force religious beliefs on workers.

A four-page draft executive order being circulated among government officials, entitled “Establishing a Government-Wide Initiative to Respect Religious Freedom,” would extend religious freedom protections to “any organization, including closely held for-profit corporations, operated for a religious purpose, even if its purpose is not exclusively religious.” A copy of the draft was obtained by The Nation.

Several progressive activists said it would sanction discrimination. Human Rights Campaign President Chad Griffin called the draft “Donald Trump’s License to Discriminate Order.”

“It reads like a wish-list from some of the most radical anti-equality activists,” Mr. Griffin said. “If Donald Trump goes through with even a fraction of this order, he’ll reveal himself as a true enemy to LGBTQ people.”

Rep. Jerrold Nadler, New York Democrat, said the draft order is “breathtaking in its scope — encouraging discrimination in social services, health care and across the federal government, creating a second class of citizenship for LGBT Americans and denying women access to constitutionally protected reproductive freedom.”

Mr. Spicer said the federal government in recent years had imposed regulations and policies that infringed on the ability of businesses and institutions to exercise their faith. He cited Hobby Lobby and Little Sisters of the Poor, court cases that successfully challenged the Obamacare mandate to provide free contraception to employees.

“There’s clearly a lot of evidence in the last couple of years of the government coming in with a lot of regulations and policies that frankly denied people the ability to live according to their faith,” said Mr. Spicer.

He discounted the purported executive order, the latest in a series of supposed drafts that he insists are not official White House documents. Mr. Spicer said that the president asks for input and ideas on a range of issues.

“But until the president makes up his mind and gives feedback and decides that that’s final, there’s nothing to announce,” he said.

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