"We do not want our internal review to complicate or impede [the FBI probe]," spokeswoman Elizabeth Trudeau said. "We are prioritizing the law enforcement investigation."
In January the department revealed that during its review of Clinton's 52,000 pages of private email it had come across 22 documents that had to be upgraded to "Top Secret" and totally withheld from public release. It said at the time that it would conduct a separate internal review to determine if the secret information in those emails had been mishandled at the time the emails were sent.
Today the State Department said it is deferring that judgment to the FBI, which is conducting a more comprehensive security review of Clinton's email. The outcome of that investigation is highly anticipated amid the 2016 election cycle. Clinton has said she is confident that will not happen and that she did not break any laws with her use of a private email server during her tenure as secretary of state.
A department spokesman said it is standard practice to allow a law enforcement agency to first complete its work before any parallel investigation is done. Trudeau called the move announced today a prudent "procedural matter."
In March the FBI responded to a formal inquiry from the State Department about how it should proceed with its internal review. It recommended that the State Department follow standard practice and put its investigation on hold.
The State Department has not ruled out conducting its own review after the FBI investigation is complete, with Trudeau saying her agency will "reassess" at the appropriate time.
The FBI is expected to interview Clinton's closest aides and the presidential candidate may also be part of its investigation. It's not clear when the investigation will be completed. The FBI has not formally named Clinton as a target and she has not been accused of any crimes.
ABC News' Mike Levine contributed to this report