FBI Director James B. Comey will reportedly remain on as head of the agency in President Trump’s administration.

The decision to keep Mr. Comey comes after the director’s disclosures about the FBI investigation into former Secretary of State Hillary Clinton’s exclusive use of a private email server ignited a political firestorm during the presidential election. It means that Mr. Comey will remain in charge of the investigatory agency as it probes alleged connections between several of Mr. Trump’s associates and the Russian government.

The New York Times first reported that Mr. Comey had told top officials within the bureau that he had been asked to stay on the job by Mr. Trump.

At a press briefing Tuesday, White House press secretary Sean Spicer said he was unable to confirm the report. An FBI spokeswoman declined to comment on the reports.

Unlike the heads of other federal agencies who resign when a new president takes office, the FBI director is appointed to a 10-year-term that is intended to run beyond more than one presidential administration.

Mr. Comey is three years into his term after being nominated for the post by former President Obama and confirmed by the Senate in 2013, but everyone from politicians to former prosecutors has raised questions about whether he should be allowed to keep his job as a result of his actions during the course of the election.

Democrats and Republicans varyingly decried or cheered each of Mr. Comey’s actions over the course of the last several months.

Republicans criticized his July announcement that the FBI would not recommend criminal charges against Mrs. Clinton, despite describing her handling of sensitive national security information as “extremely careless.”

But Democrats hit his decision to inform Congress, less than two weeks ahead of the November election, that the FBI was renewing the investigation turned the tables — with the Clinton campaign later blaming Mr. Comey’s Oct. 28 disclosure for her election loss to Mr. Trump.

Mr. Comey wrote to Congress that the FBI was renewing its investigation as a result of emails recovered as part of the sexting charges against former Rep. Anthony D. Weiner, the estranged husband of top Clinton aide Huma Abedin.

After reviewing the recovered emails, Mr. Comey again updated Congress two days before the election, saying Mr. Weiner’s computer turned up no new evidence of Clinton wrongdoing.

While both the Trump administration and the FBI have declined to comment publicly on Mr. Comey’s job status, the president greeted the FBI director fondly at a reception at the White House on Sunday. At a reception for law enforcement officials, the two men shook hands.

“He’s become more famous than me,” Mr. Trump joked.

Mr. Comey’s July announcement was a departure from typical federal law enforcement agency protocol. Officials usually decline to discuss criminal cases that are closed without criminal charges.

The FBI’s overall handling of the Clinton email investigation is now part of a wide-ranging review by the Justice Department’s inspector general.

The DOJ’s internal watchdog announced this month it would be examining several sets of accusations: that FBI policies were not followed when Mr. Comey made a series of disclosures about the investigation, that at least two agency officials should have recused themselves from involvement in the case because of close Clinton ties and that department employees may have leaked information.

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