Comey sent the letter on Sunday, just two days before the US presidental election. It followed one he sent last week saying agents would be reviewing newly discovered emails that may be connected to Clinton.
They were found on the device of Anthony Weiner, the disgraced congressman and estranged husband of Clinton's close aide Huma Abedin.
Clinton's Republican rival Donald Trump quickly responded to Comey's latest announcement, saying Clinton is protected by a "rigged system".
"Right now she's being protected by a rigged system. It's a totally rigged system. I've been saying it for a long time," Trump told supporters in Sterling Heights, Michigan.
"Hillary Clinton is guilty, she knows it, the FBI knows it, the people know it and now it's up to the American people to deliver justice at the ballot box on November 8."