Former Secretary of State Hillary Clinton delivers a keynote address during the Watermark Silicon Valley Conference for Women on February 24, 2015 in Santa Clara, California.National Journal

All or parts of 15 emails that Hillary Clinton confidante Sidney Blumenthal gave to a House committee cannot be located among the thousands of pages of emails that Clinton turned over to the State Department, the agency said Thursday night.

The State Department downplayed the discrepancy, but it's likely to intensify GOP questions and criticism about Clinton's claim that she provided State with all the work-related emails kept on her private server late last year.

"We have confirmed that the emails Secretary Clinton provided the Department include almost all of the material in Mr. Blumenthal's production. There are, however, a limited number of instances—15—in which we could not locate all or part of the content of a document from his production within the tens of thousands of emails she gave us," a department official said on condition of anonymity.

The official said, "The substance of those 15 emails is not relevant to the 2012 attacks in Benghazi."

Rep. Trey Gowdy, the GOP chairman of the committee, pounced on the revelation, stating that Clinton's unusual use of a private email account and server "has resulted in an incomplete public record."

"This confirms doubts about the completeness of Clinton's self-selected public record and raises serious questions about her decision to erase her personal server—especially before it could be analyzed by an independent, neutral third party arbiter," Gowdy said in a statement Thursday.

Nick Merrill, a spokesman for Clinton's presidential campaign, defended the completeness of her disclosure. "She has turned over 55,000 pages of materials to the State Department, including all emails in her possession from Mr. Blumenthal," Merrill said

Blumenthal, a longtime Clinton family ally who has consulted for pro-Hillary Clinton advocacy groups, sent her a suite of memos on Libyan intelligence issues in 2011 and 2012, when Clinton was secretary of State.

Blumenthal told the panel that the memos, which Clinton circulated to top aides, were written by a former high-level CIA officer.

The memos showed Blumenthal keeping Clinton abreast of his work to parry GOP attacks. In one case, an Oct. 1, 2012 email from Blumenthal to Clinton, with the subject line "H: Romney's last gambit. Got done and published. Sid.," passed along a piece in Salon about then-presidential candidate Mitt Romney's plans to go after President Obama over the Benghazi attack.

Another message passed along links to several Media Matters blog posts and noted, "Got all this done. Complete refutation on Libya smear. Philippe can circulate this links"—likely a reference to Clinton aide Philippe Reines.

According to State, the nine emails with Clinton that Blumenthal provided but State could not locate include a March 21, 2011 message with press clips about the death of one of Muammar el-Qaddafi's sons, a late August 2011 memo titled "Inside NTC latest," which is a reference to the National Transitional Council that countered the Libyan leader, and others.

Portions of six others are missing, State said.While Blumenthal provided documents that State cannot locate, the department official also noted that there are "instances where the Department has produced portions of Secretary Clinton's correspondence with Mr. Blumenthal that did not appear in his production to the Committee."

In addition to the revelation about the Blumenthal emails State could not locate, Gowdy said State "also turned over a new set of Clinton emails that were responsive to previous committee requests regarding Libya and Benghazi, but for some reason were not previously given to the committee under subpoena."

This article has been updated.

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