The State Department said Thursday that it could not locate “all or part” of 15 e-mails provided last week to the House Select Committee on Benghazi by Sidney Blumenthal from his exchanges with then-Secretary of State Hillary Rodham Clinton.

The committee chairman, Rep. Trey Gowdy (R-S.C.), who has raised repeated questions about whether Clinton covered up her activities related to the September 2012 attacks on the U.S. mission in Benghazi, Libya, called the State Department disclosure “significant and troubling.”

It was the first indication that some 55,000 pages of e-mails from a private server Clinton used while in office were not a complete record of her ­work-related correspondence, and the latest turn in what has become a contentious political battle pitting committee Republicans against Clinton and committee Democrats, who have charged Gowdy with trying to undermine her presidential campaign.

When the existence of the private server was revealed, Clinton said she had discarded “personal” e-mails and gave the rest to the State Department. The department then culled about 300 e-mails related to Benghazi in response to a committee subpoena. Many were from Blumenthal, a former Clinton White House aide and a close friend, who forwarded what he said were inside intelligence reports from sources with access to the Libyan government between 2011 and 2013. The documents, which were publicly released last month, shed no new light on the Benghazi attack.

Then-Secretary of State Hillary Rodham Clinton testifies in Washington before the Senate Foreign Relations Committee hearing on the deadly attack on the U.S. diplomatic mission in Benghazi. (J. Scott Applewhite/AP)

The committee then subpoenaed Blumenthal, who appeared for a closed-door deposition last week. He also supplied the committee with additional Libya-related e-mails that Gowdy said at the time might not have been among those culled by the State Department.

In response to a committee query, Gowdy said in a statement Thursday, “the State Department has informed the Select Committee that Secretary Clinton has failed to turn over all her Benghazi and Libya related records. This confirms doubts about the completeness of Clinton’s self-selected public record.

“This has implications far beyond Libya, Benghazi and our committee’s work,” he said, and “conclusively shows her email arrangement with herself, which was then vetted by her own lawyers, has resulted in an incomplete public record.”

An official at State, speaking on the condition of anonymity under ground rules imposed by the department, said there were “a limited number of instances — 15 — in which we could not locate all or part of the content of a document from [Blumenthal’s] production within the tens of thousands of e-mails she gave us. . . . The substance of those 15 e-mails is not relevant to the 2012 attacks in Benghazi.”

At the same time, the official said, some of the documents Clinton had already turned over “do not appear” in Blumenthal’s “production to the committee.”