WASHINGTON — The FBI’s handling of the Hillary Clinton e-mail investigation has created more turmoil for the bureau than any other matter in recent history, exposing internal tensions with the Justice Department and stirring concerns the famously apolitical organization unnecessarily injected itself into the campaign.

The FBI for decades has prided itself on being both independent and silent about its work. It has survived other painful moments in its century-long existence. But rarely have its core duties become so awkwardly entangled with politics, thanks to an election-year criminal investigation involving Clinton’s e-mail practices — and whiplash-producing public statements in the final two weeks of the campaign.

Though FBI Director James Comey signaled a conclusion to the Clinton e-mail matter with a letter to Congress on Sunday, the public isn’t done discussing it: Lawmakers demand answers to questions left unresolved by two vague and ambiguous letters. Clinton and her aides feel wronged by a curiously timed disclosure. And ex-prosecutors of both parties are concerned the bureau’s actions strayed from its mandate to remain above politics.

The controversy, coupled with a series of leaks laying bare internal squabbling, suggests a tough road ahead for FBI leadership regardless of who wins Sunday. “This has been a very difficult election process. Unfortunately, the FBI has been drawn into it,” said Leo Taddeo, a retired FBI supervisor. He said he was concerned that candidates seemed more eager than before to politicize national security issues and seek investigations into opponents.

“This is a new and developing trend in U.S. political discourse, so I think the FBI has to resist being drawn into it,” he added.

That’s easier said than done.

The FBI last year began investigating Clinton for the potential mishandling of classified information as secretary of state after a referral from the intelligence community inspector general.

When the FBI decided it wouldn’t recommend charges, he broke from protocol and delivered an unusual public statement chastising Clinton and her aides as “extremely careless.”

But the pushback to that announcement was nothing compared to what Comey has faced the last two weeks, starting with his Oct. 28 notification to Congress that the FBI would review newly discovered e-mails potentially connected to the Clinton e-mail investigation.

The statement provoked outrage from Clinton and other Democrats who said it needlessly placed her under suspicion when the FBI didn’t even know if the e-mails were important. The Justice Department opposed the idea, too.

Then came Sunday’s statement, in which Comey effectively cleared the Democratic presidential nominee by saying the new review had done nothing to change the FBI’s July recommendation that she not face charges. Though a relief to Democrats and Clinton, the news also infuriated some who wondered why the new e-mails — if apparently insignificant — were ever made public in the first place.

“Today’s letter makes Director Comey’s actions nine days ago even more troubling,” said Sen. Dianne Feinstein of California, the ranking Democrat on the Senate intelligence committee.