A highly anticipated report accuses ex-FBI Director James Comey of being "insubordinate" but not politically biased.
Clinton has blamed Comey for her election loss to Donald Trump in 2016.
The report also reveals Comey used a private email account to conduct official FBI business.
FBI director Christopher Wray said he accepted the report's findings but he added that nothing in the report pointed towards political bias or impugned the FBI as an institution.
In his report, the Inspector General criticised Comey's decision to reveal publicly a week before the election that he had reopened the inquiry into Clinton's emails, rejecting Comey's argument that he had acted in the interests of transparency.
He found that while Comey's actions were not the result of political bias, "by departing so clearly and dramatically from FBI and department norms, the decisions negatively impacted the perception of the FBI and the department as fair administrators of justice".
The 500-page report also found "a troubling lack of any direct, substantive communication" between Comey and Former Attorney General Loretta Lynch.
But the report also touched on text messages between two FBI officials who later worked on Special Counsel Robert Mueller's investigation into alleged Russian meddling in the US election.
Peter Strzok, who was Mueller's lead agent in Russian inquiry, was having an affair with Lisa Page, an FBI lawyer who also temporarily worked on the Mueller investigation.
When Page asked if Trump would become president, Strzok responded: "No. No he won't. We'll stop it."
The report called this "not only indicative of a biased state of mind but, even more seriously, implies a willingness to take official action to impact the presidential candidate's electoral prospects".
Republicans have seized on the messages to argue the FBI investigation was biased against President Donald Trump.
Christopher Wray said employees would be held accountable for any misconduct as a result of the report.
Potentially embarrassing for the former FBI director is the inspector general's finding that he used a private Gmail address to conduct some official business.
This practice continued while he was investigating Clinton for using a private email account to handle government secrets - which at the time Mr Comey branded "extremely careless".
When asked about his own email by investigators, Comey said: "I had the sense that it was OK."
He said he only handled non-confidential information on his Gmail, and it was only used for information that would become public anyway, such as speeches or public statements.
But the Inspector General said it was "inconsistent" with Justice Department policy.
Clinton took to Twitter to make a sarcastic comment.
Comey said on Twitter: "I respect the DOJ IG office, which is why I urged them to do this review. The conclusions are reasonable, even though I disagree with some. People of good faith can see an unprecedented situation differently. I pray no Director faces it again. Thanks to IG's people for hard work."
Former Attorney General Loretta Lynch released a statement outlining how the report upheld her "fidelity to the rule of law", making no mention of any of the criticism it levelled at her.
The President, meanwhile, took to Twitter to brand allegations of Russian collusion as "phony" and "garbage".
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