Trump is encouraging pastors to push politics. Here’s how that’s gotten them in trouble before.

Up for Senate reelection more than 60 years ago, Lyndon B. Johnson became gripped by fear that nonprofits were pumping large sums of cash into efforts to elect his opponent, a millionaire rancher and oilman named Dudley Dougherty.

So Johnson, a Texas Democrat, got creative.

In 1954, he pushed a new rule that would change the Internal Revenue Service tax code to say that tax-exempt nonprofits, including charities, churches and other religious groups, would be stripped of their tax status if they got involved in partisan politics, such as “directly or indirectly” supporting a candidate for office.

Since then, the Johnson Amendment has perhaps caused the greatest division among groups historians say were probably not Johnson’s prime target: houses of worship and religious leaders.

So when President Trump on Thursday signed an executive order saying he was essentially directing the IRS to stop investigating religious groups for preaching politics from the pulpit, conservative evangelicals cheered. They said it was a victory for religious freedom and free speech. They said pastors could now openly support politicians they agree with on issues like abortion and gay rights.

Conservatives also praised a section of the order designed to allow religious groups to avoid a mandate to provide contraception coverage under President Obama’s healthcare law, which would expand an exemption won through courts.

At the same time, many liberal faith leaders bemoaned the president’s move on nonprofits. They said it would weaken the separation of church and state and detract from nonpartisan traditions of faith. The Union for Reform Judaism — the largest Jewish denomination in the country — said Trump’s move could open the floodgates to turn worship services into campaign rallies.

But experts say the order, which does not change rules on the books but simply tells the IRS that it can ignore them, may not have a significant impact, largely because the anti-politicking rule has not been widely enforced.

Since 2008, at least 2,000 pastors have taken part in Pulpit Freedom Sunday, a coordinated preaching effort across the U.S. in which they challenge the ban by getting political in sermons. According to Alliance Defending Freedom, a conservative legal group that promotes the event, the IRS has only investigated one church that participated.

Since 1954, the IRS has rarely investigated nonprofits for endorsing campaigns.

Americans United for Separation of Church and State says it has reported at least 124 houses of worship to the IRS since 1996 for “unlawful political activity.” But only some of those reports have resulted in IRS warnings or investigations and fewer have led groups to lose their tax status.

In 2004, the IRS launched a program called the Political Activities Compliance Initiative that investigated at least 82 religious groups for endorsing partisan politics in election cycles through 2008. But enforcement has slowed since 2009, when the IRS lost a lawsuit in Minnesota against the Living Word Christian Center, which had endorsed Republican Michele Bachmann to represent Minnesota in Congress. A judge tossed out the suit on a technicality.

In a document that was released as part of a 2014 lawsuit filed by the Freedom from Religion Foundation based in Madison, Wis., the IRS wrote to the Department of Justice that there were 99 churches that merited “a high priority examination” for violations between 2010 and 2013. It’s not clear whether all 99 were investigated.

Here are some of the most prominent cases in which the Johnson Amendment was applied.

Branch Ministries, New York

In 1992, Branch Ministries, a church that operated under the name the Church at Pierce Creek, ran ads in newspapers including the Washington Times and USA Today against presidential candidate Bill Clinton.

“Christians Beware. Do not put the economy ahead of the Ten Commandments,” said the ads, which were published four days before the presidential election. “Bill Clinton is promoting policies that are in rebellion to God’s laws.”

“Tax-deductible donations for this advertisement gladly accepted,” said fine print in the ads.

The federal government’s investigation into the organization lasted through 1995, when its tax-exempt status was revoked.

The National Assn. for the Advancement of Colored People

In July 2004, NAACP President Julian Bond criticized President George W. Bush in a speech, saying the president’s administration sowed racial divisions in the United States.

The IRS launched an inquiry later that year. Bond said he thought it was politically motivated.

Nearly two years after it started looking into the group, the IRS said the organization “continued to qualify” for its tax status.

“It was an enormous threat,” Bond, who died in 2015, said in a news report on the investigation. “The opposite outcome would have reduced our income remarkably.”

He said he interpreted the investigation’s conclusion to mean that the IRS “thought they had harassed us enough and they could stop.”

All Saints Episcopal Church, Pasadena

Two days before the 2004 presidential election, a guest speaker at All Saints Episcopal Church in Southern California gave a sermon in which he pitted Jesus debating against presidential candidates George W. Bush and John F. Kerry.

The Rev. George F. Regas, the church’s former rector, did not make an endorsement. He said “good people of profound faith” could vote for Bush or Kerry. But he also strongly criticized the Iraq war and said Jesus would have said Bush’s Iraq strategy had “led to disaster.”

The IRS opened an investigation into the sermon the next year, and wrote a letter to the church saying investigators thought the priest’s words were illegal.

The agency’s accusation was based on its reading of a Los Angeles Times article from the time of the sermon. The article contained three paragraphs about Regas’ words in a summary of Sunday sermons ahead of the election.

IRS officials wrote to the church in 2007 to say they had concluded the investigation. The IRS said it still thought the church had tried to influence votes but that officials would not revoke the church’s tax exemption.

The Rev. Edward J. Bacon Jr., who was the rector at the time, says he disagrees with Trump’s executive order.

“If you are going to be a Christian you will have to engage in policy advocacy, but there is a difference between partisan advocacy and politics. That is how we prevailed,” said Bacon, who left the church last year and lives in Birmingham, Ala. “We had a very clear line between advocating for policies that were for ‘the least of these,’ which is essential to our faith, and the endorsement of any candidate. What we had done was criticized policies of officeholders.”

Franklin Graham organizations

In 2013, the Rev. Franklin Graham, son of the Rev. Billy Graham, wrote a letter to President Obama saying he believed the IRS was targeting two of his organizations for their conservative positions on social issues.

Graham said his charities, the Billy Graham Evangelistic Assn. and Samaritan’s Purse, received letters the year before saying they were under examination. The IRS did not indicate why it was looking into the groups and it’s not clear that the Johnson Amendment was applied. But Graham said they were targeted because of advertisements run under their names. One ad was against same-sex marriage and another encouraged people to vote for “candidates who base their decisions on biblical principles and support the nation of Israel.”

Graham, who advised Trump during his campaign, believed the IRS inquiry was part of a broader effort in which conservatives said the IRS was delaying the processing of paperwork and targeting groups with the phrase “tea party” and “patriot” in their names.

“After the election, we did receive official notice that our organizations continue to qualify for exemption from federal income tax, and that our returns were accepted as filed. Unfortunately, while these audits not only wasted taxpayer money, they wasted money contributed by donors for ministry purposes, as we had to spend precious resources servicing the IRS agents in our offices.… This is morally wrong and some would call it ‘un-American,’” Graham wrote.

jaweed.kaleem@latimes.com