WASHINGTON — President Obama sharply criticized the decision by his F.B.I. director to alert Congress on Friday about the discovery of new emails related to the Hillary Clinton server case, implying that it violated investigative guidelines and trafficked in innuendo.

“We don’t operate on incomplete information,” Mr. Obama said in an interview with NowThis News, broadcast Wednesday. “We don’t operate on leaks. We operate based on concrete decisions that are made.”

“When this was investigated thoroughly the last time, the conclusion of the F.B.I., the conclusion of the Justice Department, the conclusion of repeated congressional investigations was that she had made some mistakes but that there wasn’t anything there that was prosecutable,” Mr. Obama said.

The president did not mention the F.B.I. director, James B. Comey, but it was clear Mr. Obama was referring to him.

Declaring that he had “made a very deliberate effort to make sure that I don’t look like I’m meddling in what are supposed to be independent processes for making these assessments,” Mr. Obama nonetheless expressed confidence in Mrs. Clinton.

“I trust her,’’ he said. “I know her. And I wouldn’t be supporting her if I didn’t have absolute confidence in her integrity and her interest in making sure that young people have a better future.’’

White House officials later downplayed Mr. Obama’s remarks about the F.B.I. and insisted he had not meant to criticize Mr. Comey.

“The president went out of his way to say he wouldn’t comment on any particular investigations,” Eric Schultz, a White House spokesman, told reporters on Air Force One while Mr. Obama was en route to North Carolina to campaign for Mrs. Clinton. Mr. Schultz characterized Mr. Obama’s remarks as mirroring those made in recent days by the White House press secretary, Josh Earnest, who had said that while the White House would not criticize Mr. Comey’s decision to update Congress on the status of an ongoing investigation, Mr. Obama believed that rules intended to keep such investigations confidential were good ones and should be followed.

For the last several days, the F.B.I. has been analyzing emails belonging to Huma Abedin, a top adviser to Mrs. Clinton. Agents discovered the emails last month in an unrelated investigation into Ms. Abedin’s estranged husband, the disgraced former congressman Anthony D. Weiner.

In a letter to Congress, Mr. Comey said those emails might be pertinent to the investigation into Mrs. Clinton’s use of a private email server. Authorities concluded that case in July with no charges. But the letter, sent over the objection of the Justice Department, led to controversy because it deviated from longstanding guidelines.

Mr. Obama took a more pointed tone than his press secretary, Josh Earnest, who said on Tuesday that the White House did not have an official position on Mr. Comey’s decision. Mr. Earnest referred to the Justice Department guidelines, however, and said, “The president believes that it’s important for those guidelines and norms to be followed.”

It is increasingly unlikely that agents will finish their work on the emails by Election Day, F.B.I. officials said. They said there was a chance they could offer updates before next Tuesday.

The renewed interest in Mrs. Clinton’s emails — a matter she believed she had put behind her months ago — has exploded in the final days of the presidential campaign, with recent polls showing that the race is tightening. But Mrs. Clinton remains ahead of her Republican challenger, Donald J. Trump, in most national polls to date.

Much is unknown about the new emails, including why they were on Mr. Weiner’s laptop in the first place. Ms. Abedin, through her lawyers, has adamantly denied using that laptop, which people with knowledge of the matter have said was identified in court papers as a Dell model. People with knowledge of the matter have said that the emails may have ended up on the laptop because they were inadvertently backed up or downloaded onto an older computer and then transferred from the older computer to the laptop’s hard drive when the older computer was replaced.

Mr. Obama first commented publicly on the investigation last year before the F.B.I. had determined that neither Mrs. Clinton nor her aides would face charges for mishandling classified information found on the secretary of state’s private email server. The president’s remarks angered F.B.I. agents who said he was prejudging the investigation.

“I don’t think it posed a national security problem,” Mr. Obama said on “60 Minutes” on CBS in October 2015. He said it had been a mistake for Mrs. Clinton to use a private email account when she was secretary of state, but his conclusion was unmistakable: “This is not a situation in which America’s national security was endangered.”