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WASHINGTON — The commissioner of the Internal Revenue Service, John A. Koskinen, expressed regret Wednesday for management mistakes, but called the attempt by House Republicans to impeach him “improper,” warning that such threats would discourage people from government service.

“A lot of people are going to say, ‘Why should I risk my career or my reputation to do public service?’ in that context,” Mr. Koskinen told the House Judiciary Committee, at its third hearing to consider arguments by conservatives in Congress that he be removed from office.

He also rejected Republican calls for him to resign, but said he would leave office if the next president so wishes. Otherwise, Mr. Koskinen’s term ends in November 2017.

The commissioner fielded hostile questions or comments from Republicans for nearly four hours at the hearing, which was scheduled last week by House leaders to persuade conservatives to shelve their demand for an immediate impeachment vote by the full House. No executive branch official below the cabinet rank has ever been impeached, and not even a cabinet member has faced such proceedings in 140 years.

With Congress hoping to recess next week for election campaigning, the issue could well be moot.

Conservatives seeking to oust Mr. Koskinen say they might still try to force a House vote. But lawmakers in both parties said an impeachment resolution would most likely fail, given bipartisan sentiment that the commissioner should be able to know the charges against him, submit his own evidence and cross-examine witnesses.

Senate Republicans have said they will not take up a House impeachment resolution. It would be up to the Senate to try Mr. Koskinen on any charges leveled by the House. But senators instead have praised him for his varied government career going back decades.

At issue is Mr. Koskinen’s response after the 2013 disclosure that I.R.S. employees, since 2010, had subjected mainly conservative groups to extra scrutiny and delays in handling their applications for tax-exempt status as “social welfare” entities — or 501(c)4s based on the pertinent tax code provision.

Groups that are strictly political are not eligible to be tax exempt. But as the Tea Party movement emerged as a conservative force, I.R.S. employees began using that phrase, among others, to flag applications for attention. Conservatives charged that the Obama administration was targeting their groups illegally, though several investigations have blamed management and bureaucratic failures, not political motives.

The controversy predated Mr. Koskinen’s arrival as commissioner. Five top I.R.S. officials, including the acting commissioner, lost their jobs, and President Obama brought Mr. Koskinen, 77, out of retirement to head the beleaguered agency in December 2013. Within months, however, he was answering allegations that he had allowed subpoenaed records to be destroyed, failed to quickly notify Congress and then mistakenly testified that all information had been provided.

At the Judiciary hearing on Wednesday, Mr. Koskinen again testified that the destruction of emails was inadvertent, and that his testimony in 2014 was based on what he thought was factual at the time. But he expressed regrets.

“The truth is, we did not succeed in preserving all of the information requested. And some of my testimony later proved mistaken,” Mr. Koskinen said. He added, “Even closer communication with Congress would have been advisable.”

“I have an overall record at the I.R.S. that I’m proud of,” he said, while acknowledging that it was up to Congress to judge.

A number of Republicans did, and they condemned him.

“All we’re asking is this guy no long hold this office,” said Representative Jim Jordan of Ohio, a leader of the conservative House Freedom Caucus, which has led the push to impeach Mr. Koskinen.

Mr. Jordan brandished a recent court opinion that suggested that the I.R.S. was still singling out conservative groups, but Mr. Koskinen denied that. Mr. Jordan also derided Mr. Koskinen’s statements, supported by investigators, that two employees on a night shift at an I.R.S. facility in Martinsburg, W.Va., had inadvertently destroyed some of the records Congress sought — calling it “the ol’ midnight-shift-guys-in-Martinsburg excuse.”

Representative Steve Chabot of Ohio said Mr. Koskinen had “betrayed the country, and most sadly got away with it.” Like other Republicans, he said the I.R.S. would never give taxpayers the benefit of the doubt that the agency itself seeks.

Several Democrats denounced the hearings as a “sham,” and many changed the subject, instead asking Mr. Koskinen leading questions in reference to the Republican presidential nominee, Donald J. Trump.

While Mr. Koskinen said he could not talk about any specific taxpayer, he said the I.R.S. would not object to someone releasing tax returns under audit — as Mr. Trump has suggested the I.R.S. would do in refusing to release his own returns. Mr. Koskinen also described violations of tax law by charitable foundations in hypothetical terms, much like critics have alleged against Mr. Trump’s foundation.

“I appreciate your being here to clear some of that up,” said Representative Ted Deutch, Democrat of Florida.

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