The Obama administration confirmed for the first time Friday that Hillary Clinton's unsecured home server contained closely guarded government secrets, censoring 22 emails with material requiring one of the highest levels of classification. The revelation comes just three days before the Iowa presidential nominating caucuses in which Clinton is a candidate.
Department officials also said the agency's Diplomatic Security and Intelligence and Research bureaus will investigate whether any of the information was classified at the time of transmission, going to the heart of one of Clinton's primary defenses of her email practices.
The State Department will release its next batch of emails from Clinton's time as secretary of state later Friday.
But The Associated Press learned seven email chains are being withheld in full from the Friday release because they contain information deemed to be "top secret." The 37 pages include messages recently described by a key intelligence official as concerning so-called "special access programs" — a highly restricted subset of classified material that could point to confidential sources or clandestine programs like drone strikes or government eavesdropping.
"The documents are being upgraded at the request of the intelligence community because they contain a category of top secret information," State Department spokesman John Kirby told the AP, describing the decision to withhold documents in full as "not unusual." That means they won't be published online with the rest of the documents, even with blacked-out boxes.
Department officials wouldn't describe the substance of the emails, or say if Clinton sent any herself.
Clinton, the front-runner for the Democratic presidential nomination, has insisted she never sent or received information on her personal email account that was classified at the time. No emails released so far were stamped "CLASSIFIED" or "TOP SECRET," but reviewers previously had designated more than 1,000 messages at lower classification levels for public release. Friday's will be the first at the top secret level.
Even if Clinton only read, and didn't write or forward the secret messages, she still would have been required to report classification slippages that she recognized. But without classification markings, that may have been difficult, especially if the information was in the public domain.
"We firmly oppose the complete blocking of the release of these emails," Clinton campaign spokesman Brain Fallon said in a statement. "Since first providing her emails to the State Department more than one year ago, Hillary Clinton has urged that they be made available to the public. We feel no differently today."
Fallon accused the "loudest and leakiest participants" in a process of bureaucratic infighting for withholding the exchanges. The documents, he said, originated in the State Department's unclassified system long before they ever reached Clinton, and "in at least one case, the emails appear to involve information from a published news article."
"This appears to be overclassification run amok," Fallon said.
Kirby said the State Department was focused, as part of the Freedom of Information Act review of Clinton's emails, on "whether they need to be classified today." Questions about their past classification, he said, "are being, and will be, handled separately by the State Department."
Possible department responses for classification infractions include counseling, warnings or other action, State Department officials said, though they declined to say if these applied to Clinton or senior aides who've since left the department. The officials weren't authorized to speak on the matter and spoke on condition of anonymity.
Separately, Kirby said the department also was withholding eight email chains, totaling 18 messages, between President Obama and Clinton. These are remaining confidential "to protect the president's ability to receive unvarnished advice and counsel," but will ultimately be released like other presidential records.
Friday's release is coming at an awkward time for Clinton. The Iowa caucus is on Feb. 1, and her main challenger, Vermont Sen. Bernie Sanders, is running a competitive campaign in Iowa and New Hampshire. Clinton still holds a strong advantage in national polls.
The emails have been an issue for Clinton's campaign since it became known 10 months ago that she exclusively used a nongovernment account linked to a homebrew server while in office. Clinton first called the decision a matter of convenience and then termed it a mistake, even if doing so wasn't expressly forbidden. But the matter could prove more troublesome now that Clinton's former agency has confirmed that business conducted over the account included top-secret matters.
Like Clinton, the State Department discounted such a possibility last March. Both also said her account was never hacked or compromised. Security experts assess that as unlikely, and that the vast majority of her emails were preserved properly for archiving purposes because she corresponded mainly with government accounts. They've backtracked from the archiving claim, while the AP discovered several phishing attempts on her server connected to Russia.
The question of special access programs first surfaced last week, when Charles I. McCullough, the inspector general for US intelligence agencies, cited examples on Clinton's account in a letter to Congress. Republicans pounced on the report, though Clinton's campaign insisted none of the exchanges were "classified at the time" and accused McCullough and GOP lawmakers of selectively leaking materials to damage her presidential hopes.
Kirby confirmed that the "denied-in-full emails" are among those McCullough recently cited. One of the emails, he said, was among those McCullough identified last summer as possibly containing top secret information.
The AP reported last August that one focused on a forwarded news article about the classified US drone program run by the CIA. Such operations are widely discussed in the public sphere, including by top U.S. officials, and the State Department immediately argued with McCullough's claim. The other concerned North Korean nuclear weapons programs, according to officials.
At the time, several officials from different agencies suggested the disagreement over the drone emails reflected the government's tendency to overclassify material, and the lack of consistent policies across difference agencies about what should and shouldn't be classified.
The FBI also is looking into Clinton's email setup, but has said nothing about the nature of its probe. Independent experts say it is highly unlikely that Clinton will be charged with wrongdoing, based on the limited details that have surfaced up to now and the lack of indications that she intended to break any laws.
"What I would hope comes out of all of this is a bit of humility" and an acknowledgement from Clinton that "I made some serious mistakes," said Bradley Moss, a Washington lawyer who regularly handles security clearance matters.
Legal questions aside, it's the potential political costs that are probably of more immediate concern for Clinton. She has struggled in surveys measuring her perceived trustworthiness and an active federal investigation, especially one buoyed by evidence that top secret material coursed through her account, could negate one of her main selling points for becoming commander in chief: Her national security resume.