On Friday, James Comey, the director of the Federal Bureau of Investigation, acting independently of Attorney General Loretta Lynch, sent a letter to Congress saying that the F.B.I. had discovered e-mails that were potentially relevant to the investigation of Hillary Clinton’s private server. Coming less than two weeks before the Presidential election, Comey’s decision to make public new evidence that may raise additional legal questions about Clinton was contrary to the views of the Attorney General, according to a well-informed Administration official. Lynch expressed her preference that Comey follow the department’s longstanding practice of not commenting on ongoing investigations, and not taking any action that could influence the outcome of an election, but he said that he felt compelled to do otherwise.

Comey’s decision is a striking break with the policies of the Department of Justice, according to current and former federal legal officials. Comey, who is a Republican appointee of President Obama, has a reputation for integrity and independence, but his latest action is stirring an extraordinary level of concern among legal authorities, who see it as potentially affecting the outcome of the Presidential and congressional elections.

“You don’t do this,” one former senior Justice Department official exclaimed. “It’s aberrational. It violates decades of practice.” The reason, according to the former official, who asked not to be identified because of ongoing cases involving the department, “is because it impugns the integrity and reputation of the candidate, even though there’s no finding by a court, or in this instance even an indictment.”

Traditionally, the Justice Department has advised prosecutors and law enforcement to avoid any appearance of meddling in the outcome of elections, even if it means holding off on pressing cases. One former senior official recalled that Janet Reno, the Attorney General under Bill Clinton, “completely shut down” the prosecution of a politically sensitive criminal target prior to an election. “She was adamant—anything that could influence the election had to go dark,” the former official said.

Four years ago, then Attorney General Eric Holder formalized this practice in a memo to all Justice Department employees. The memo warned that, when handling political cases, officials “must be particularly sensitive to safeguarding the Department’s reputation for fairness, neutrality, and nonpartisanship.” To guard against unfair conduct, Holder wrote, employees facing questions about “the timing of charges or overt investigative steps near the time of a primary or general election” should consult with the Public Integrity Section of the Criminal Division.

The F.B.I. director is an employee of the Justice Department, and is covered by its policies. But when asked whether Comey had followed these guidelines and consulted with the Public Integrity Section, or with any other department officials, Kevin Lewis, a deputy director of public affairs for the Justice Department, said, “We have no comment on the matter.”

According to the Administration official, Lynch asked Comey to follow Justice Department policies, but he said that he was obliged to break with them because he had promised to inform members of Congress if there were further developments in the case. He also felt that the impending election created a compelling need to inform the public, despite the tradition of acting with added discretion around elections. The Administration official said that Lynch and Justice Department officials are studying the situation, which he called unprecedented.

Matthew Miller, a Democrat who served as the public-affairs director at the Justice Department under Holder, recalled that, in one case, the department waited until after an election to send out subpoenas. “They didn’t want to influence the election—even though the subpoenas weren’t public,” he said. “People may think that the public needs to have this information before voting, but the thing is the public doesn’t really get the information. What it gets is an impression that may be false, because they have no way to evaluate it. The public always assumes when it hears that the F.B.I. is investigating that there must be something amiss. But there may be nothing here at all. That’s why you don’t do this.”

“Comey is an outstanding law-enforcement officer,” Miller said, “but he mistakenly thinks that the rules don’t apply to him. But there are a host of reasons for these rules.”

As Miller sees it, Comey’s “original sin” was the press conference he held in July regarding the Clinton e-mail investigation. At that press conference, Comey stated that the F.B.I. had found no reason to bring criminal charges against Clinton for using a private e-mail server to handle much of her State Department business, but that Clinton and her staff had been “extremely careless in their handling of very sensitive, extremely classified information.” Comey made clear that he had decided to make this comment without any sign-off from the Justice Department. Ordinarily, when no charges are brought, such matters are not exposed to public view, let alone addressed at press conferences.

Comey’s supporters argue that he had to act independently, and publicly, because Lynch had compromised herself by having an impromptu visit with Bill Clinton late in the investigation. In the ensuing uproar, Lynch promised to accept Comey’s recommendation on whether to bring charges against Clinton. But, as Miller notes, Comey’s press conference triggered a series of other events, including congressional hearings where Comey was forced to defend his decision not to recommend prosecution. Comey’s letter to Congress on Friday updated his earlier statements that the Clinton e-mail investigation had ended.

In a letter to F.B.I. employees sent soon after the letter to Congress, Comey tried to explain his unusual decisions. In the letter, which was obtained by the Washington Post, he acknowledged, “Of course, we don’t ordinarily tell Congress about ongoing investigations, but here I feel an obligation to do so given that I testified repeatedly in recent months that our investigation was completed. I also think it would be misleading to the American people were we not to supplement the record. At the same time, however, given that we don’t know the significance of this newly discovered collection of emails, I don’t want to create a misleading impression. In trying to strike that balance, in a brief letter and in the middle of an election season,” he noted, “there is significant risk of being misunderstood.”

“I don’t really blame Comey,” another former Justice Department official said. “But it’s troubling.” This official thought that Comey “didn’t want to look tainted. This new information comes to him, and he’s afraid if he doesn’t make it public until after the election he’ll be impeached. People will say he lied to Congress. But in the end he did the self-protective thing. Was it the right thing? Put it this way: it isn’t what previous Administrations have done.”