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Ms. Lerner has refused to testify to Congress, citing her Fifth Amendment right to remain silent. But committee Republicans have said she waived that right by declaring her innocence to the committee, and they have said they will consider recalling her.

In addition to probes from Congress, the Justice Department also opened an investigation into the matter. Ms. Lerner’s attorney has said she would testify if lawmakers were willing to erase any potential legal jeopardy.

In a statement Wednesday, the IRS said the chief counsel’s office is consulted on decisions when applications for tax-deductible status are going to be rejected, but that is the extent of the office’s responsibility.

“Otherwise, operating division personnel make the ultimate decisions on disposition of particular cases. Those decisions take into account legal advice from counsel attorneys, but they are not controlled by that advice,” the agency said in its statement. “Counsel attorneys do not control cases unless and until they are docketed for litigation in the United States Tax Court.”

The IRS has acknowledged asking intrusive questions of tax-exempt groups and of delaying many of their applications for far too long.

Democrats have said progressive groups also were given special scrutiny, which they said shows the IRS wasn’t engaged in political targeting but rather was trying to sort through groups in the wake of the Supreme Court ruling.

Rep. Elijah E. Cummings of Maryland, the ranking Democrat on the oversight committee, released a memo Tuesday that included other excerpts of interviews with IRS employees who scoffed at charges of political targeting.

“Despite an extremely aggressive investigation involving thousands of documents and more than a dozen interviews of IRS employees, the overwhelming evidence before the committee reveals no political motivation or White House involvement in this process,” Mr. Cummings said.

On Wednesday, Mr. Cummings accused the Republican chairmen of skewing the story by giving only small snapshots of the interviews.

“Rather than describing the whole truth, your letter appears yet again to create a skewed account based on partial, incomplete, and cherry-picked information while disregarding key evidence that contradicts your political narrative,” he wrote in a letter to oversight committee Chairman Darrell E. Issa, California Republican.