The legislation comes on the heels of the FBI's announcement on Tuesday that it would not recommend criminal charges against Clinton, the presumptive Democratic presidential nominee, for her use of a private email server and address to send State Department emails.
The investigation is restarting following the decision by the Justice Department not to pursue a criminal investigation, spokesman John Kirby said.
The State Department said in April it had suspended plans for an internal review at the request of the Federal Bureau of Investigation, which conducted a yearlong probe of Clinton's use of private email servers while she was secretary of state.
Kirby set no deadline for the investigation's completion.
Kirby wouldn't say anything more about the precise information officials are evaluating.
Among the likely topics of such a review will be whether Clinton or her aides should have their security clearances revoked because they discussed classified information on an unsecured computer system.
But after FBI Director James Comey announced earlier on Wednesday that there was not enough evidence to prosecute Hillary Clinton, the State Department decided it was time it resumed its own investigation.
Clinton now has a "top secret/special access programme" clearance - the highest - which the State Department renewed in 2013, two years after she resigned as secretary of state, according to correspondence between the State Department and Congress.
"Our goal will be to be as transparent as possible about our results, while complying with our various legal obligations", Kirby said.
Kirby told the Associated Press that former officials can still face "administrative sanctions".
Hillary Clinton - and some of her most trusted senior advisors - will twist in the wind a while longer.
Now that inquiry is over, the State Department will reopen its review.
While the most serious outcome - loss of security clearance - seems impossible (bordering on absurd) to enforce on Mrs Clinton were she to be elected president, it could prevent her from placing any affected staff into high levels of her administration.
FBI Director James Comey testifies Thursday on Capitol Hill.
"So, we have asked for them to go back through any employee that was connected to this, whether that be Huma Abedin, whether that be all the different individuals that are on the email chains and series of chains and say their security clearance should be removed". "The Inspector General of the State Department has come through and said she clearly violated the rules".
Congressman Frank Lucas, R-OK, said based on the FBI's findings, he is very disappointed Comey did not recommend that the Justice Department hold Clinton accountable for her actions.