The IRS’s inspector general confirmed Thursday it is conducting a criminal investigation into how Lois G. Lerner’s emails disappeared, saying it took only two weeks for investigators to find hundreds of tapes the agency’s chief had told Congress were irretrievably destroyed.

Investigators have already scoured 744 backup tapes and gleaned 32,774 unique emails, but just two weeks ago they found an additional 424 tapes that could contain even more Lerner emails, Deputy Inspector General Timothy P. Camus told the House Oversight Committee in a rare late-night hearing meant to look into the status of the investigation.

“There is potential criminal activity,” Mr. Camus said.

He said they have also discovered the hard drives from the IRS’s email servers, but said because the drives are out of synch it’s not clear whether they will be able to recover anything from them.

“To date we have found 32,744 unique emails that were backed up from Lois Lerner’s email box. We are in the process of comparing these emails to what the IRS has already produced to Congress to determine if we did in fact recover any new emails,” Mr. Camus said.

Democrats questioned the independence of Inspector General J. Russell George, who is overseeing the investigation, saying he’s injected politics into his work.

Rep. Gerald Connolly, Virginia Democrat, said Mr. George is refusing to turn documents over to him, prompting a heated reply.

“You’re not entitled to certain documents,” Mr. George said.

“Oh really? We’ll see about that, won’t we,” Mr. Connolly replied, saying that he questioned whether Mr. George could be trusted if he’s refusing to provide documents, yet is in charge of an investigation into whether the IRS stonewalled document requests.

The hearing was the latest chapter in the complex investigation into the IRS’s targeting of tea party groups for special scrutiny.

Several congressional committees are still probing the matter, and both the inspector general and the Justice Department are conducting criminal investigations.

In a 2013 report, the inspector general said the IRS had improperly targeted conservative and tea party groups’ applications for nonprofit status, asking repeated intrusive questions and delaying their applications well beyond a reasonable time. Some of those groups are still waiting, with their applications now pending for years.

Rep. Jason Chaffetz, Utah Republican and Oversight Committee chairman, said the ongoing investigations undercut President Obama’s assertion last year that there was no evidence of corruption in the IRS’s targeting.

“I have no idea how the president came to such a definitive conclusion without all the facts,” he said.

The IRS belatedly told Congress it may have lost some of Ms. Lerner’s emails after her computer crashed, and asserted that the backup tapes didn’t exist.

But under questioning from Mr. Chaffetz, Mr. Camus said it took him only two weeks to track down the backup tapes, and when he asked the IRS depository for them, the workers there said they’d never been contacted by the agency itself.

Republicans said that was stunning because IRS Commissioner John Koskinen repeatedly assured Congress the emails were irretrievably lost.

“I think they have misled or lied to the committee,” said Rep. John L. Mica, Florida Republican.

Mr. Camus said they were clued in to the 424 new tapes they just found a couple of weeks ago after realizing the IRS hadn’t given over a key document. They demanded that document, and realized it showed hundreds of other tapes existed.

Democrats said the investigation has dragged on too long and been too expensive, pointing to the IRS’s estimate that it has spent $20 million on staff and equipment to try to comply with the committee’s request.

Ms. Lerner, who oversaw the unit of the IRS that scrutinized nonprofit groups’ applications, is a central figure in the investigations.

After belatedly discovering that some of her emails weren’t being recovered, the IRS did try to reconstitute them by asking other employees to dig through their emails to see if they were the recipients of any messages that involved her. That did produce some of the missing emails.

Democrats said the GOP seemed to be insinuating Ms. Lerner had purposely crashed her hard drive to hide emails — though she herself pushed to try to get messages recovered.

Democrats also questioned why the hearing was happening now, given that Mr. Camus and Mr. George both stressed that their findings are preliminary and could change as they learn more.

“It seems that the best course of action would be to have the inspector general come back when his report is complete,” said Rep. Elijah E. Cummings of Maryland, the ranking Democrat on the panel.

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