WASHINGTON — President Trump lashed out at the F.B.I. on Sunday, defending himself after the guilty plea by his former national security adviser, Michael T. Flynn, by charging that the bureau’s reputation was “in tatters — worst in history” and denying that he had told his first F.B.I. director to end the Flynn investigation.

Two and a half hours after he began tweeting on Sunday morning, he continued by quoting a news headline in all caps: “ANTI-TRUMP FBI AGENT LED CLINTON EMAIL PROBE.”

James B. Comey, the former F.B.I. director, testified before Congress in May that Mr. Trump had asked him to drop the inquiry into Mr. Flynn one day after Mr. Trump had fired Mr. Flynn. Mr. Comey declined to do so, and the president fired him several months later.

In a 6:15 a.m. tweet on Sunday, the president called Mr. Comey a liar and said the news media had spread falsehoods.

The president’s comments came two days after Mr. Flynn pleaded guilty to lying to the F.B.I. about his conversations with the Russian ambassador. Mr. Flynn agreed to cooperate with Robert S. Mueller III, the special counsel investigating Russian election interference.

In an extraordinary attack on the top law enforcement body in his own government, Mr. Trump accused the F.B.I. and its career investigators of having a bias against him.

He said in a tweet that the agency’s reputation was in ruins because of Mr. Comey’s tenure, during which the F.B.I. conducted what he called the “phony and dishonest” investigation into the private email server used by his rival in the 2016 election, Hillary Clinton.

Mr. Trump’s efforts to shift the attention to Mrs. Clinton after Mr. Flynn’s guilty plea began Saturday night, when he assailed the Justice Department.

“Many people in our Country are asking what the ‘Justice’ Department is going to do about the fact that totally Crooked Hillary, AFTER receiving a subpoena from the United States Congress, deleted and ‘acid washed’ 33,000 Emails?” he wrote, referring to messages that Mrs. Clinton’s lawyers had deemed unrelated to her government work. “No justice!”

On Sunday, the president also seized on revelations that earlier this summer Mr. Mueller reassigned one of his top investigators on the Russia inquiry because of concerns that the agent, Peter Strzok, had sent text messages that showed a bias against Mr. Trump.

Mr. Trump also retweeted two Twitter posts about Mr. Strzok, including one urging Christopher A. Wray, the current F.B.I. director, to “clean house” at the agency because of the revelations about Mr. Strzok.

And for the second time in 12 hours, the president took note of ABC News’s decision to suspend Brian Ross, a top investigative reporter, after Mr. Ross erroneously reported on Friday that Mr. Flynn would testify that the president had directed him to talk with Russians during the campaign. Mr. Flynn told investigators that he was directed to talk with Russians during the transition, after the election.

Reacting to a drop in the stock market after Mr. Ross’s erroneous report, Mr. Trump urged investors to sue ABC.

Two and a half hours after he began tweeting on Sunday morning, he continued by quoting a news headline in all caps: “ANTI-TRUMP FBI AGENT LED CLINTON EMAIL PROBE.”