In meetings since then between Mr. Trump and pastors, whether in public or private, Mr. Moore said, Mr. Trump consistently says, “Everybody in this country has freedom of speech, except for you.”

Churches and clergy members are free to speak out on political and social issues — and many do — but the Johnson Amendment was intended to inhibit them from endorsing or opposing political candidates.

Separately, the Free Speech Fairness Act was introduced in the House and the Senate on Wednesday. The bill would modify the Johnson Amendment by allowing churches and other charities to engage in political expression.

However, most Americans, and even most clergy members, say they do not want churches and houses of worship to engage in partisan politics. Nearly 80 percent of Americans said it was inappropriate for pastors to endorse a candidate in church, and 75 percent said churches should not make endorsements, according to a survey released in September by LifeWay Research, an evangelical polling group based in Nashville.

Moreover, 87 percent of pastors said they should not make political endorsements from the pulpit, according to a LifeWay survey conducted in 2012 of pastors in evangelical and mainline Protestant churches. (Clergy members who were Republicans were slightly more in favor of endorsements than those who were Democrats or independents.)

Pastors and churches that endorsed candidates have seemed to have little to fear from the I.R.S. The overburdened agency has little capacity to investigate every report of a violation — and there have been many.

But only one church is known to have ever lost its tax-exempt status for partisan politicking, and that was in 1995, those on all sides said. It is impossible to know how many churches the I.R.S. has investigated. The agency does not make public when it investigates a church for violations, and an I.R.S. spokesman declined to answer questions related to the Johnson Amendment on Thursday.