FBI director James Comey’s decision to reopen an investigation into Hillary Clinton’s email server 11 days before the election shook up the race.
The Department of Justice (DoJ) Inspector General Michael Horowitz said he would look into “certain actions” by the FBI and DoJ.
Mrs Clinton was cleared of any wrongdoing days before the US voted.
Her campaign team has blamed the FBI announcement as a key factor why she lost the election to Donald Trump.
The announcement on Thursday does not mention Hillary Clinton by name but refers to public disclosures by Mr Comey.
Mr Horowitz said his review would look at a news conference in July 2016 when Mr Comey said he would not recommend charges for Mrs Clinton.
A letter to Congress on 28 October, in which Mr Comey said there were more emails to look at, will also be subject to this new inquiry.
An explosive move – Anthony Zurcher, BBC News, Washington
It seems the 2016 election isn’t going to go gently into that good night. Thanks to this decision by the Justice Department inspector general, one of the more controversial moments of the recently concluded presidential campaign is going to be given closer scrutiny.
Hillary Clinton and her campaign team say FBI Director James Comey’s two interventions close to election day cost her the presidency. It certainly knocked the Democrat off her stride and dominated headlines, allowing Donald Trump – who had been staggered by sexual harassment allegations – to regain his political footing.
They also contend that the action violated Justice Department guidelines and was an overtly partisan act from a law enforcement agency that should be apolitical. Perhaps they will view this announcement as bittersweet vindication.
The scope of the review covers more than just Mr Comey’s actions throughout the campaign, however. It will also address concerns expressed by Republicans that some lower-level FBI officials may have improperly shared information with the Clinton campaign.
Depending on how this investigation is conducted, and the conclusions it draws, the fuse may have just been lit on a stick of political dynamite that will explode later in the year.
The inspector general said his investigation had come in response to “numerous” requests from the public and from members of Congress.
Mrs Clinton said she had set up a home email server for reasons of convenience, but admitted it was a mistake.
In clearing her in July, the FBI said Mrs Clinton and her staff were “extremely careless” in handling classified materials.
But there was no evidence of intentional wrongdoing, it said.
Then in October they briefly reopened the investigation after finding new related emails from top Clinton aide Huma Abedin.
They were found on a laptop belonging to her estranged husband, disgraced former congressman Anthony Weiner, but nothing was found on them and the case was closed for a second time.