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Todd Shearer, a spokesman for the Billy Graham Evangelistic Association, said Mr. Obama never responded to the letter.

Michelle Easton, president of the Clare Boothe Luce Policy Institute, said her group was unfairly targeted.

“I can only conclude that our mission of preparing and promoting conservative women leaders must have been seen as a threat to this administration,” Ms. Easton said. “This audit ensured we were occupied by government agents and diverted from our mission of helping young women.”

Mr. Blackwell said his institute, which trains young conservatives, also underwent an IRS audit in 1996 that costs his group $70,000 in attorney fees.

This time, the IRS focused on the 2008 tax year. The audit began in the summer of 2011 and ended more than a year later.

Mr. Blackwell said his group paid $50,000 in attorney fees and provided more than 23,000 pages of documents in order to comply with the audit.

Last week, an IRS employee told Congress that Lois Lerner, the former head of the Exempt Organizations Division, demanded that he send some of the reviews of tea party groups to the IRS chief counsel’s office in Washington. The chief counsel is one of two political appointees in the IRS.

Mr. George also rejected Democratic efforts to portray his investigation as partisan, saying IRS officials withheld key information about a lookout list for some liberal groups until last week. Mr. George’s numbers indicate that far more of the 298 political groups seeking tax-exempt status during the 2010 and 2012 elections singled out for intrusive scrutiny had “tea party” or other conservative labels in their names. None of the cases used “occupy” in the name, while just seven had “progress” or “progressive.”