Senior Justice Department officials warned FBI Director James Comey against talking about current criminal investigations or being seen as meddling in elections.

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WASHINGTON — The day before the FBI director, James Comey, sent a letter to Congress announcing new evidence had been discovered that may be related to the completed Hillary Clinton email investigation, the Justice Department strongly discouraged the step and told him he would be breaking with longstanding policy, three law-enforcement officials said Saturday.

Senior Justice Department officials did not move to stop him from sending the letter, officials said, but they did everything short of it, pointing to policies against talking about current criminal investigations or being seen as meddling in elections.

That Comey proceeded despite those protests highlights the unusual nature of Friday’s revelations, which added a dramatic twist to the final days of the presidential campaign. His action also reignited a firestorm that Clinton believed she had put behind her when the FBI decided in July not to charge anyone in the investigation into the handling of classified information on her private email server while she was secretary of state from 2009 until 2013. Comey’s letter did not reopen that inquiry.

Senior Justice Department officials, career prosecutors and some in the FBI were at a loss Saturday as to what would happen next. Would Comey provide a blow-by-blow accounting of the FBI’s steps until Election Day? Did he plan further announcements? Or did he intend, after shaking up the election with his letter, to remain silent about the facts until the presidential votes had been tallied? The FBI offered no comment, and Justice Department officials said they had no idea what Comey saw as his next move.

Justice Department officials were particularly puzzled about why Comey had alerted Congress — and by extension, the public — before agents even began reading the newly discovered emails to determine whether they contained classified information or added new facts to the case.

The letter to Congress — which followed the discovery of a new batch of emails during an investigation into Anthony Weiner, a disgraced former Democratic congressman from New York — opened Comey up to criticism from Democrats and from current and former officials at the FBI and the Justice Department, including Republicans. Weiner is the estranged husband of Huma Abedin, a longtime aide to Clinton

“There’s a longstanding policy of not doing anything that could influence an election,” said George Terwilliger III, a deputy attorney general under President George H.W. Bush. “Those guidelines exist for a reason. Sometimes, that makes for hard decisions. But bypassing them has consequences.”

He added, “There’s a difference between being independent and flying solo.”

The letter is also the latest example of an at-times strained relationship between the Justice Department and Comey, who technically answers to the attorney general but who — on issues of race, encryption and, most notably, the Clinton investigation — has branded himself as someone who operates outside D.C.’s typical chain of command.

After hearing the Justice Department’s concerns, Comey concluded the ramifications of not telling Congress promptly about the new emails outweighed concerns about the department guidelines, one senior law-enforcement official said.

Under Justice Department policy, restated each election cycle, politics should play no role in any investigative decisions. In Democratic and Republican administrations, Justice Department officials have interpreted that policy broadly, to cover any steps that might give even an impression of partisanship.

“We must be particularly sensitive to safeguarding the department’s reputation for fairness, neutrality and nonpartisanship,” the deputy attorney general, Sally Yates, wrote in a memo this year.

After reports surfaced late last month in a British tabloid that Weiner had sent sexually explicit text messages to a 15-year-old girl in North Carolina, top prosecutors in Charlotte, N.C., and Manhattan jockeyed for the case.

Senior officials in the Justice Department decided that if there were a prosecution, it would take place in New York under the supervision of the U.S. attorney there, Preet Bharara.

About the same time, agents in the FBI’s New York field office understood that the Weiner investigation could possibly turn up additional emails related to Clinton’s private server, according to a senior federal law-enforcement official, because of the Abedin-Weiner link. Abedin and Weiner separated this year after Weiner was caught in 2011, 2013 and again this year sending numerous woman sexually explicit texts and photographs of himself undressed.

On Oct. 3, FBI agents seized several electronic devices from Weiner: a laptop, his iPhone and an iPad that was in large measure used by his 4-year-old son to watch cartoons, a person with knowledge of the matter said. Days later, FBI agents also confiscated a Wi-Fi router that could identify any other devices that had been used, the person said.

While searching the laptop, agents discovered tens of thousands of emails, some of them sent between Abedin and other Clinton aides, according to senior law-enforcement officials. It is not clear if Abedin downloaded the emails to the laptop or if they were automatically backed up there. The emails dated back years, the officials said.

Abedin told lawyers in a June deposition for a civil lawsuit over State Department records that she never deleted old emails, either at work with Clinton or at home with Weiner. “I didn’t have a practice of managing my mailbox other than leaving what was in there sitting in there,” Abedin said. “I didn’t go into my emails and delete State.gov emails. They just lived on my computer. That was my practice for all my email accounts.”

Because of the age of the newly discovered emails, many could be outside the scope of the Clinton inquiry, investigators said. And while many are probably duplicative, some would be worth reading, the FBI. concluded.

Senior Justice Department and FBI officials agreed the matter was worth pursuing. By law, though, agents and prosecutors in the Clinton investigation could not immediately read the new emails without court authority.

The authorities decided only recently to seek that approval. They do not know whether the emails contain classified information or, if they do, whether that would change their determination that nobody should be charged with mishandling it.

So Justice Department officials were surprised Thursday afternoon to receive notice of intention to send the letter to Congress. The letter, issued as early voting is under way in some states, guaranteed a new round of questions for Clinton just before Election Day.

Comey sent the letter Friday to Congress; the letter said emails had surfaced in a case unrelated to the Clinton case. Comey said the FBI would review the emails to determine if they improperly contained classified information, adding that the emails “appear to be pertinent.”

Comey, who had faced mounting criticism in recent months from Republicans for not recommending that Clinton or her aides be charged with a crime, immediately came under attack from Democrats. They charged that just 11 days before an election, he was unnecessarily inserting himself into politics.