NEW YORK » For the past three years, the Internal Revenue Service hasn’t been investigating complaints of partisan political activity by churches, leaving religious groups who make direct or thinly veiled endorsements of political candidates unchallenged.

The IRS monitors religious and other nonprofits on everything from salaries to spending, and that oversight continues. However, Russell Renwicks, a manager in the IRS Mid-Atlantic region, recently said the agency had suspended audits of churches suspected of breaching federal restrictions on political activity. A 2009 federal court ruling required the IRS to clarify which high-ranking official could authorize audits over the tax code’s political rules. The IRS has yet to do so.

Dean Patterson, an IRS spokesman in Washington, said Renwicks, who examines large tax-exempt groups, “misspoke.” Patterson would not provide any specifics beyond saying that “the IRS continues to run a balanced program that follows up on potential noncompliance.”

However, attorneys who specialize in tax law for religious groups, as well as advocacy groups who monitor the cases, say they know of no IRS inquiries in the past three years into claims of partisanship by houses of worship. IRS church audits are confidential, but usually become public as the targeted religious groups fight to maintain their nonprofit status.

“The impression created is that no one is minding the store,” said Melissa Rogers, a legal scholar and director of the Center for Religion and Public Affairs at Wake Forest University Divinity School in North Carolina. “When there’s an impression the IRS is not enforcing the restriction — that seems to embolden some to cross the line.”

The issue is closely watched by a cadre of attorneys and former IRS officials who specialize in tax-exempt law, along with watchdog groups on competing sides of the church-state debate.

Americans United for Separation of Church and State, which seeks strict limits on religious involvement in politics, and the Alliance Defending Freedom, which considers the regulations unconstitutional government intrusion, scour the political landscape for any potential cases. While Americans United gathers evidence it hopes will prompt an IRS investigation, the Alliance Defending Freedom jumps in to provide a defense. Neither group knows of any IRS contact with houses of worship over political activity since the 2009 federal ruling.

Nicholas Cafardi, a Duquesne University Law School professor and Roman Catholic canon lawyer who specializes in tax-exempt law, said he has heard of no IRS inquiries over churches and politics in the last three years. Neither has Marcus Owens, a Washington attorney who spent a decade as head of the IRS tax-exempt division and is now in private practice.

Owens, who was with the IRS through 2000, said the agency had once initiated between 20 and 30 inquiries each year concerning political activity by churches or pastors. He said he knows of only two recent cases the IRS pursued against houses of worship or pastors, and neither involved complaints over partisan activity.

“What the IRS is desperate to do is to avoid signaling to churches and pastors that there is no administrative oversight,” Owens said. “The IRS has been vigilant with regard to civil fraud and criminal cases, but those aren’t all that common.”

The tax code allows a wide range of political activity by houses of worship, including speaking out on social issues and organizing congregants to vote. But churches cannot endorse a candidate or engage in partisan advocacy. The presidential election has seen a series of statements by clergy that critics say amount to political endorsements. Religious leaders say they are speaking about public policies, not candidates, and have every right to do so.

The Billy Graham Evangelistic Association has recently taken out full-page ads in major newspapers, featuring a photo of renowned evangelist Billy Graham, urging Americans to vote along biblical principles. Graham met last month with Mitt Romney and pledged to do “all I can” to help the Republican presidential nominee.

In a survey last week by the Pew Forum on Religion and Public Life, 40 percent of black Protestants who attend worship services regularly said their clergy have discussed a specific candidate in church — and the candidate in every instance was President Barack Obama.

This Sunday, Roman Catholic Bishop Daniel Jenky of Peoria, Ill., ordered all the priests in his diocese to read a statement urging Catholics to vote and stating that, “Catholic politicians, bureaucrats, and their electoral supporters who callously enable the destruction of innocent human life in the womb also thereby reject Jesus as their Lord.”

In Texas, a pastor of a small independent church posted a sign on the front of the building that read, “Vote for the Mormon, not the Muslim.” Romney is the first Mormon nominee for president by a major party. Opponents of Obama, who is Christian, have spread false rumors that he is Muslim.

Renwicks made his comments Oct. 18, at a Washington seminar on tax-exempt organizations presented by the American Law Institute-Continuing Legal Education. Responding to a moderator’s question about the status of church audits, Renwicks said, “we’re basically holding any potential church audits — they’re basically in abeyance.

“I haven’t done a church audit in quite some time,” said Renwicks, according to a recording of the talk provided by the American Law Institute. “There were one or two — what I’d call somewhat, maybe potentially egregious cases — where I thought maybe, we need to go out there, but even those were put in abeyance until we get the signature issue resolved.”

An IRS reorganization in 1998 put responsibility for authorizing the audits in the hands of lower-ranking IRS officials. A Minnesota pastor, who faced an audit over his 2007 endorsement from the pulpit of Rep. Michele Bachmann, argued the IRS was violating its own rules. In 2009, a federal judge agreed, prompting a formal IRS rule-making process that continues today.

Dean Zerbe, a former senior counsel to the Senate Finance Committee who specializes in tax fraud and abuse, said the audits are “an extremely hellish area for the IRS to deal with.”

The agency has to balance enforcement with churches’ First Amendment rights. Even when the federal agency finds an outright violation, the penalty for houses of worship is usually little more than a warning. The IRS has revoked nonprofit status in just a handful of these cases since the rules for religious groups were adopted in 1954.

Last month, more than 1,500 pastors, organized by the Alliance Defending Freedom, endorsed a candidate from the pulpit and then sent a record of their statement to the IRS, hoping their challenge would eventually end up in court. The Alliance has organized the event, called “Pulpit Freedom Sunday,” since 2008. The IRS has never contacted a pastor involved in the protest.

“I think people are misled to think the IRS wakes up every morning wanting to knock on the door of a church or synagogue,” said Zerbe. “Most senators blanch at the idea of having an IRS agent in the pews listening to what’s going on from the pulpit. … I think the IRS in some ways reflects that similar discomfort.”