In July, State Department officials installed a safe at the office of attorney David Kendall after the government determined some of Clinton's emails may have contained classified information. But it said last week the safe wasn't suitable for so-called top secret, sensitive compartmented information, known as TS/SCI, which the government has said was found in some messages.
Assistant Secretary of State Julia Frifield wrote to Senate Judiciary Committee Chairman Charles Grassley on Sept. 22 that "while the safe was suitable for up to (top secret) information, it was not approved for TS/SCI material" because the material wasn't held in a facility set up for discussing highly secret information, known as a SCIF, or sensitive compartmented information facility.
Those questions were not an issue at the time the safe was installed because "there was no indication that the emails might contain TS or TS/SCI material," Frifield wrote in the letter obtained by The Associated Press. Kendall has a top secret security clearance.
The State Department's letter underscores how even the nation's diplomatic apparatus didn't anticipate Clinton, a Democratic presidential candidate, would have sent or received such highly sensitive information on her private email server while secretary of state. Questions about her use of such a server have at times dominated her White House run.
Kendall and a Clinton spokesman did not immediately return messages seeking comment Monday.
"It shows how badly the wires were crossed" between the State Department, which didn't anticipate any of the emails would be top secret, and the intelligence community, which decided they were classified, said Steven Aftergood, a government secrecy expert at the Federation of American Scientists.
The State Department also said it was unaware of whether anyone's security clearances were suspended pending an investigation into possible improper handling of classified information, one of several questions posed by Grassley, R-Iowa. Such an action is not uncommon amid such classification reviews, said Bradley Moss, a Washington lawyer who deals regularly with security clearance matters.
The AP in March first discovered that Clinton ran her server off an Internet connection traced to her Chappaqua, New York, home. Clinton later confirmed she operated the server for convenience but did not provide details on how well the basement server was backed up or how adequately it was protected from hackers.
Since then, the State Department has indicated through Freedom of Information Act releases of Clinton's emails that dozens of messages that passed through her private server were later deemed classified. Most messages released so far have been marked "confidential," the lowest level of U.S. government classification.
But two emails, although not marked classified at the time they were sent, have since been slapped with a "TK" marking, for the "talent keyhole" compartment, suggesting material obtained by spy satellites, according to the inspector general for the intelligence community. They also were marked "NOFORN," meaning information that can only be shared with Americans with security clearances.
One email included a discussion of a U.S. drone strike, part of a covert program that is nevertheless widely known. A second conversation could have improperly referred to highly classified material, but it also could have reflected information collected independently, U.S. officials who have reviewed the correspondence told the AP.
Clinton has since apologized for using a private server and said she's provided copies of all the messages she was required to turn over. She reiterated in a recent interview that she didn't "send or receive any material marked 'classified.' We dealt with classified material on a totally different system. I dealt with it in person."
Since earlier this year, government investigators — and her political adversaries in particular — have focused on Clinton's email practices that effectively bypassed government-run systems. Also potentially at issue is whether Clinton withheld any work-related emails from the roughly 30,000 messages she provided to the State Department.
The AP is one of several organizations that have sued the State Department for records during her tenure, including emails to and from Clinton and her former top aides.