The letter to Congress came two days before the presidential election pitting the Democratic nominee against Republican Donald Trump. The former secretary of state's use of a private email server has been at the forefront of a bitter campaign.
"Based on our review, we have not changed our conclusions that we expressed in July," Comey said in the letter to top Republicans on the House Oversight Committee.
The letter served as a "supplement" to his Oct. 28 letter that the FBI would be further investigating Clinton's use of a personal email server.
"Since my letter, the FBI investigative team has been working around the clock to process and review a large volume of emails from a device obtained in connection with an unrelated criminal investigation," Comey wrote Sunday. "During that process we reviewed all of the communications that were to or from Hillary Clinton while she was secretary of state ... I am very grateful to the professionals at the FBI for doing an extraordinary amount of high-quality work in a short period of time."
During a separate investigation of Anthony Weiner, the estranged husband of top Clinton aide Huma Abedin, the FBI found emails that could be connected to its investigation of whether Clinton mishandled classified information by using a private email server. The emails were discovered on a laptop used by Weiner to allegedly send sex-related messages to a 15-year-old girl. Investigators found 650,000 emails on Weiner's laptop.
"We went through this as fast as we could," a senior law enforcement official told CNN.
The emails were mostly duplicates of ones the FBI had already seen and personal emails, the source said.
On July 5, the FBI announced it was not recommending criminal charges against Clinton.
Clinton spokesman Brian Fallon said Sunday on Twitter, "We were always confident nothing would cause the July decision to be revisited. Now Director Comey has confirmed it."
And then he tweeted: "We're glad this issue is resolved but for the record, this could easily have been learned before 1st letter was sent."
Kellyann Conway, Trump's campaign manager, responded on Twitter, "Then why did you, your colleagues and your candidate attack Comey and his credibility?
Trump alluded to the latest letter during a rally.
"You have to understand, it's a rigged system," he said at a rally in Minneapolis. "And she's protected."
Current House Speaker Paul Ryan, a Republican, said in a statement, "Regardless of this decision, the undisputed finding of the FBI's investigation is that Secretary Clinton put our nation's secrets at risk and in doing so compromised our national security. Fortunately, the American people have the opportunity to ensure Secretary Clinton never gets her hands on classified information again."
Democrats on Capitol Hill praised Comey's decision.
"While the original letter should never have been sent so close to an election, the expeditious review of these emails should put to rest -- once and for all -- the irresponsible speculation indulged in by the Trump campaign and others," Rep. Adam Schiff, the top Democrat on the House Intelligence Committee said in a letter. "Voters can now make their decision based on the merits, and that decision should be simple: It is the choice between a woman superbly qualified to be commander in chief and a man patently unfit for office."