Representing the religious leaders are three Washington attorneys, all former IRS officials, who also filed a complaint accusing defense fund attorneys of violating IRS rules by helping the churches break federal law.
Meanwhile, a separate group of 180 ministers, rabbis and imams also has sought to counter the "pulpit initiative."
Members of the Interfaith Alliance -- which includes the nation's top Episcopal bishop -- have signed a pledge to refrain from electioneering in their houses of worship.
"Political activity and political expressions are very important, but partisan politics are . . . . a death knell to the prophetic freedom that any religious organization must protect," said the Rev. Ed Bacon, rector of All Saints Episcopal Church in Pasadena, who signed the pledge.
All Saints survived a nearly two-year IRS investigation after former Rector George Regas spoke out against the Iraq war on the eve of the 2004 presidential election. Bacon repeatedly said the church did not engage in campaigning. The IRS dropped the case last year even though agency officials indicated that they still considered the sermon to be illegal.
All Saints leaders voiced frustration Wednesday at pulpit initiative backers for using the Pasadena church's fight with the IRS as fodder for their cause.
"These people are wanting to promote one candidate over another and that's a huge difference," Bacon said.
At the heart of the controversy is the Johnson amendment, named after former President Lyndon Johnson, a senator from Texas when it was enacted in 1954. The measure stated that nonprofit, tax-exempt organizations cannot participate in political campaigns for or against candidates for public office.
Many churches have appeared to step over the line, but legal scholars could recall only one church that lost its tax-exempt status -- a congregation in New York that urged voters not to vote for Bill Clinton in the 1992 presidential race.
The defense fund said churches targeted by the IRS would serve as clients for lawsuits against the agency in federal court.
The defense fund issued seemingly contradictory statements about the initiative. On one hand, it insists pastors will not endorse candidates and will simply exercise their constitutional rights by addressing "the differing positions of the presidential candidates in light of Scripture."