The Wisconsin-based Freedom From Religion Foundation on Wednesday filed a lawsuit against the IRS for failing to audit thousand of churches that allegedly violated federal tax law by engaging in partisan advocacy.

“[T]he Internal Revenue Service, under the direction of the Defendant Shulman, has followed and continues to follow a policy of non-enforcement of the electioneering restrictions of §501(c)(3) against churches and other religious organizations,” the lawsuit states. “As a result, in recent years, churches and religious organizations have been blatantly and deliberately flaunting the electioneering restrictions of §501(c)(3), including during the presidential election year of 2012.”

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The Internal Revenue Code prohibits 501(c)(3) organizations, including churches and charities, from intervening or participating in political campaigns. However, an IRS official recently said the agency had halted audits of churches engaging in political activity in the last three years. A federal court ordered the IRS to clarify who could authorize the audit of churches in 2009, but the agency has not yet adopted new regulations.

“We are holding any potential church audits in abeyance,” IRS official Russell Renwicks said.

The IRS later disavowed the statement, insisting the agency intended to investigate the many complaints it had received once it revised its regulations.

“The IRS continues to run a balanced program that follows up on potential non-compliance, while ensuring the appropriate oversight and review to determine that compliance activities are necessary and appropriate,” IRS spokesman Dean Patterson clarified.

The Freedom From Religion Foundation said in its lawsuit that failing to enforce electioneering restrictions on churches was a violation of the Establishment Clause of the First Amendment and of the group’s equal protection rights.

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More than 1,000 pastors said they openly defied the IRS by telling their congregation to vote for a particular presidential candidate on October 7. The event, dubbed “Pulpit Freedom Sunday,” was organized by the conservative Christian group Alliance Defending Freedom in an attempt to prompt legal action over the tax code.

[Preacher holding Bible via Shutterstock]