"We are expressing our view to Justice that no charges are appropriate in this case," he said.
But Comey note clear shortcomings in security protocols for the emails, which include 50 in "classified" categories with eight "top secret."
"Although we did not find clear evidence that Secretary Clinton or her colleagues intended to violate laws governing the handling of classified information, there is evidence that they were extremely careless in their handling of very sensitive, highly classified information," Comey said.
The timing will provide fodder for Clinton's opponents.
Early last week, former president Bill Clinton had an impromptu meeting with U.S. Attorney General Loretta Lynch aboard Lynch's plane at an airport in Phoenix.
Lynch asserted they did not discuss any pending investigations, but the conversation sparked an uproar - with some Republicans and Clinton rivals calling for a third party to be appointed to handle the case.
On Friday, Lynch announced that she would accept recommendations from career prosecutors and FBI agents leading the probe - a decision that she said had been made before her meeting with Bill Clinton, but one that was surely meant to quiet criticism about the independence of the probe.
The investigation had been focused on whether classified information was mishandled because Clinton used a private email account when she was secretary of state. The former secretary of state had asserted she "never received nor sent any material that was marked classified," although she said that some might have been retroactively branded classified during the process to prepare it for public release.