Comey said Clinton and her team were "extremely careless," but added that there was not clear evidence that they intended to violate the law. That appears to clash with Clinton's view of her habits, as she replied "no" when asked by CNBC in March if her email practices were sloppy.
"There was not a single one of those that was marked classified," she said.
However, Comey said the investigation showed that 110 emails in 52 email chains were determined to include classified information at the time they were received.
Clinton and her staff could have violated certain laws even if they did not intend to do so, said Jacob Frenkel, a former Department of Justice attorney. He said possible ignorance or negligence can still lead to charges in some cases.
"I think the Department of Justice senior prosecutors certainly can review this. And I think there is a basis for the Department of Justice to come to a different conclusion," he told CNBC's "Squawk Alley."
In a statement after Comey's remarks, a Clinton spokesman said the campaign is "pleased" with the announcement.
"As the Secretary has long said, it was a mistake to use her personal email and she would not do it again. We are glad that this matter is now resolved," the statement said.
Reactions from Clinton's Republican opponents also showed they may use the FBI's findings as attack fodder even if she is not charged. Presumptive Republican nominee Donald Trump seized on Comey's assessment as more evidence of a "rigged" political system.
In a statement, Republican National Committee Chairman Reince Priebus said the findings "are a glaring indictment of Hillary Clinton's complete lack of judgment, honesty and preparedness to be our next commander in chief."
The Clinton campaign did not immediately respond to a request for comment on the differences between her comments to CNBC in March and the conclusions of the FBI investigation.
— CNBC's Everett Rosenfeld contributed to this report.