The IRS sent one of its intrusive scrutiny letters to a nonprofit group in order to throw up a smokescreen and prevent the group from complaining to Congress about poor treatment, according to one of Lois G. Lerner’s apparently lost emails, which were recovered by auditors and released by an interest group Tuesday.

Judicial Watch, which sued to force the production of the Lerner emails, said the emails confirm that Ms. Lerner, the central figure in the targeting probe, and her colleagues were aware of the sensitive nature of the cases but appeared to hide details of the massive backlog they were amassing as they held up hundreds of tea party and conservative group applications for nonprofit status.

The IRS turned over 906 pages of emails July 15 to Judicial Watch, a conservative public interest law firm, ahead of a Wednesday court hearing. Judicial Watch concluded that the emails were part of the messages Ms. Lerner lost in a computer malfunction, and released them Tuesday. “This material shows that the IRS’ cover-up began years ago,” said Tom Fitton, president of Judicial Watch. “We now have smoking-gun proof that top officials in the Obama IRS unlawfully harassed taxpayers just to keep them from complaining to Congress about IRS’ targeting and abuse. No wonder the Obama IRS has had such little interest in preserving or finding Lois Lerner’s emails.”

The Lerner emails have become almost as big a scandal as the initial targeting. Ms. Lerner, who was head of the division that scrutinized the tea party applications until she retired while under investigation in 2013, suffered a computer hard drive crash that cost potentially thousands of emails that should have been part of the record. The IRS took routine steps to try to recover the emails but reported that it was unable to do so.

But the agency’s independent inspector general said it was able to find the messages easily on backup tapes stored at remote locations — and that the IRS never bothered to look for those tapes, even as it was telling Congress that all possible routes for message recovery had been exhausted.

According to the new emails, Ms. Lerner and her colleagues were aware of the growing outcry among nonprofit groups that they were being delayed. In one Nov. 3, 2011, exchange between Ms. Lerner and Cindy Thomas, a program manager in the Cincinnati office that was handling the cases and was involved in a back-and-forth with Washington, the IRS admitted to having hundreds of cases stacked up and awaiting action. Afraid of congressional pressure, Ms. Thomas ordered one of the inquiry letters to be sent, just to prevent one of the organizations being held up from complaining. “Just today, I instructed one of my managers to get an additional information letter out to one of these organizations — if nothing else to buy time so he didn’t contact his Congressional Office,” she wrote in the email released by Judicial Watch. Ms. Thomas said she feared a judge would get involved soon and order the IRS to move the applications more quickly.

That email exchange did confirm that IRS employees in Washington were deeply involved in making decisions about the nonprofit groups’ cases. The IRS initially blamed the Cincinnati office for the glitch.

President Obama last week blamed the targeting scandal not on poor management but on “crummy” legislation he said Congress passed that gave his employees confusing instructions, and on funding cuts. He said the IRS wasn’t able to do its best work as a result. “Congress has passed a crummy law that didn’t give people guidance in terms of what they were trying to do. They did it poorly and stupidly,” Mr. Obama told “Daily Show” host Jon Stewart.

A number of the 906 pages of emails released to Judicial Watch are redacted, with the agency citing the “b5” exemption under the Freedom of Information Act, which allows the government to withhold information deemed to be part of the agency deliberative process. The IRS claimed other pages that were withheld contained sensitive taxpayer information — including what appear to be published news articles.

On Monday, Republicans on the House Committee on Oversight and Government Reform called Mr. Obama to oust Ms. Lerner’s successor, IRS Commissioner John Koskinen, for obstructing the targeting investigation.

Chairman Jason Chaffetz, Utah Republican, said Mr. Koskinen gave assurances that the IRS would save email that was key to the investigation at the same time the emails were being destroyed. “The reality is what he said was false. He repeatedly made false statements,” Mr. Chaffetz said at a Capitol Hill press conference, where he was joined by more than a dozen fellow Republicans from the committee. “Mr. Koskinen should no longer be the IRS commissioner,” said Mr. Chaffetz. “Mr. Koskinen failed in his duty to preserve and produce documentation to this committee.”

The IRS defended Mr. Koskinen. “The record is clear that the IRS and Commissioner Koskinen have been cooperative and truthful with the numerous investigations underway. The agency has produced more than one million pages of documents in support of the investigations, provided 52 current and former employees for interviews and participated in more than 30 Congressional hearings on these issues,” the agency said in a statement.

The IRS inspector general has concluded that the agency did in fact target conservative and tea party groups for intrusive scrutiny, and the Justice Department is still conducting a criminal investigation into the targeting.

Mr. Chaffetz noted that 24,000 potential emails were destroyed after the materials were under subpoena and after the agency’s chief technology officer issued a preservation notice ordering employees not to destroy anything. The chief technology officer later told the committee that he was “blown away” that backup tapes were destroyed 10 months after his preservation notice.