The State Department learned the email record was incomplete after U.S. lawmakers investigating the deadly 2012 attack on diplomatic staff in Benghazi, Libya, were given several previously undisclosed emails discussing Libya by Sidney Blumenthal, an old friend and informal adviser to Clinton.
"There are ... a limited number of instances 15 in which we could not locate all or part of the content ...," the State Department official said in an email. "The substance of those 15 emails is not relevant to the 2012 attacks in Benghazi."
Most government workers are required to use government email addresses, and Clinton's unusual use of a private email address connected to a server in her home while working as the top U.S. diplomat has exposed her to criticism that she side-stepped record-keeping and transparency rules.
Trey Gowdy, the Republican congressman in charge of the select committee investigating the Benghazi attack, said Clinton's incomplete email record "raises serious questions".
"This has implications far beyond Libya, Benghazi and our committee's work," Gowdy said in a statement. "This conclusively shows her email arrangement with herself, which was then vetted by her own lawyers, has resulted in an incomplete public record."
Spokesmen for Clinton have declined to answer questions about her email records since evidence of the gaps first emerged last week when Gowdy's committee released the additional emails provided by Blumenthal.
In March, Clinton said in an impromptu news conference at the United Nations headquarters that she gave the State Department all her emails that "could possibly be work-related".
She said that the 30,490 emails she handed over included all that referred to Libya or Benghazi, and included all work-related correspondence from what her office described as "long-time friends".
Most of the 15 previously undisclosed messages between Blumenthal and Clinton were in the form of long memoranda filled with intelligence on the turmoil in Libya.
Blumenthal could not immediately be reached for comment.
State Department says can't locate 15 Hillary Clinton emails
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