The IRS did mishandle tea party and conservative groups’ nonprofit applications, but their behavior didn’t break any laws, the Justice Department said in a letter to Congress Friday that cleared the tax agency and former senior executive Lois G. Lerner of any crimes.

“Ineffective management is not a crime,” Assistant Attorney General Peter J. Kadzik said in a letter to the House Ways and Means Committee. “The Department of Justice’s exhaustive probe revealed no evidence that would support a criminal prosecution. What occurred is disquieting and may necessitate corrective action — but it does not warrant criminal prosecution.”

The decision comes more than two years after the IRS’s internal watchdog reported that auditors singled out tea party groups’ applications for special scrutiny and delayed those applications beyond reasonable timelines, preventing the groups from being able to say they were officially recognized nonprofits.

The agency initially admitted its bad behavior, and President Obama vowed an investigation — but he later said, in the middle of the probe, that there was no evidence of corruption.

Some Republicans have questioned the validity of the probe from the beginning, after learning that one of the Justice Department lawyers assigned to the investigation was a contributor to Mr. Obama’s political campaigns.

In its letter Friday the Justice Department specifically cleared Ms. Lerner, a senior executive in charge of approving the groups’ applications, who had authored a number of emails that suggested a bias against the tea party movement.

Investigators said none of the witnesses they interviewed believed Ms. Lerner acted out of political motives, and said that Ms. Lerner seemed to try to correct the inappropriate scrutiny once she “recognized that it was wrong.”

“In fact, Ms. Lerner was the first IRS official to recognize the magnitude of the problem and to take concerted steps to fix it,” Mr. Kadzik wrote.

Congressional Democrats said the decision confirmed what they’d figured out years ago — that there was no underhanded political dealing at the agency.

“Over the past five years, Republicans in the House of Representatives have squandered literally tens of millions of dollars going down all kinds of investigative rabbit holes — IRS, Planned Parenthood, Benghazi — with absolutely no evidence of illegal activity,” said Rep. Elijah E. Cummings of Maryland, the top Democrat on the Benghazi investigation and ranking member of the House Oversight Committee.

The House Ways and Means Committee conducted its own investigation into the IRS’s tea party targeting, as did the Senate Finance Committee. The House panel was the one that voted to refer Ms. Lerner’s behavior to the Justice Department for criminal investigation.

Rep. Paul Ryan, the chairman of the Ways and Means Committee, called the Friday letter “deeply disappointing,” but said it wasn’t a surprise given the bent of the Obama administration.

He said his committee’s probe did find “serious and unprecedented actions” by Ms. Lerner that deprived tea party groups of their rights.

“The American people deserve better than this. Despite the DOJ closing its investigation, the Ways and Means Committee will continue to find answers and hold the IRS accountable for its actions,” he said.

Ms. Lerner’s lawyers, in a statement, said they were “gratified but not surprised” by the announcement.

“Anyone who takes a serious and impartial look at the facts would reach the same conclusion as the Justice Department,” they said, adding that she cooperated with the investigators and answered their questions.

That stands in contrast to her interaction with Congress, where she refused to answer questions, invoking her Fifth Amendment right to remain silent — but only after she delivered a statement declaring her innocence.

The House Oversight Committee concluded that she was not, in fact, able to invoke the Fifth Amendment at that point, and when she refused to answer questions, the House voted to hold her in contempt of Congress.

The Justice Department declined to pursue that case, too, arguing that her claim of Fifth Amendment rights was likely to succeed.

Groups that faced targeting by the IRS were infuriated by Friday’s decision.

“To say there is no evidence of discrimination makes a mockery of all we witnessed in the last two years,” said Catherine Engelbrecht, founder of True the Vote, which had its application for nonprofit status delayed as it and another group she was involved in faced scrutiny by everyone from the FBI to federal occupational health authorities.

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