A Fox News Channel investigation appears to challenge presumptive Democratic presidential nominee Hillary Clinton’s insistence that “nothing” she sent or received on a private e-mail server was classified when she was secretary of State.

“Hillary Clinton, from the moment her exclusive use of personal email for government business was exposed, has claimed nothing she sent or received was marked classified at the time,” write Fox News Channel security analysts Catherine Herridge and Pamela Browne, in a new report published Saturday.

“But a 2012 email released by the State Department appears to challenge that claim because it carries a classified code known as a ‘portion marking’ — and that marking was on the email when it was sent directly to Clinton’s account.”

The analysts found that a “C” — which means the message was marked classified at the confidential level — is in the left-hand-margin. It relates to an April 2012 phone call with Malawi’s first female president, Joyce Banda, who took power after the death of President Mutharika in 2012.

The message reads “(C) Purpose of Call: to offer condolences on the passing of President Mukharika and congratulate President Banda on her recent swearing in.”

The rest of the message was fully redacted before it was publicly released by the State Department — “a sign that the information was classified at the time and dealt with sensitive government deliberations,” Ms. Herridge and Ms. Browne noted.

A U.S. government source told them that there are other Clinton emails with classified markings, or marked classified, beyond the April 2012 document.

The analysts also refer to a 2014 federal government training manual, which provides a clear guide for reviewing classified information and allocating classified codes or “portion markings.”

The manual requires that the marking “be uniformly and conspicuously applied to leave no doubt about the classified status of the information, the level of protection required, and the duration of classification.”

According to the guide, “Portion markings consist of the letters ‘(U)’ for Unclassified, ‘(C)’ for Confidential, ‘(S)’ for Secret, and ‘(TS)’ for Top Secret.”

On Wednesday, Mrs. Clinton previously told Fox News “Special Report” anchor Bret Baier, “The fact is, nothing that I sent or received was marked classified, and nothing has been demonstrated to contradict that.”

Rep. Mike Pompeo, a member of the House Intelligence Committee who has read the 22 top secret emails too damaging to national security to release, did not speak directly to Fox News about the new report, though he acknowledged the possibility that there could be a conflict.

He did, however, issue a statement on Saturday after the report was released.

“After the Benghazi Committee discovered Hillary Clinton’s private email server, we heard a variety of explanations as to why she did not use the official and secure State Department system, and what types of emails she housed on this system,” Mr. Pompeo noted.

“First her answer was, ‘I did not email any classified material to anyone on my email.’ As new facts emerged, she was forced to update her talking points. Her latest version has been, ‘Nothing I sent or received was marked “classified”,’” the Kansas Republican said.

“Newly discovered communication seriously calls into question her version of the facts. It appears very evident that Secretary Clinton sent and received classified information that was marked as such and that was ultimately stored on her homebrewed server,” Mr. Pompeo said.

“This is the latest revelation in what is becoming an avalanche of falsities from our country’s former top diplomat. I call on Hillary Clinton to finally come clean about her mishandling of classified information and to tell the truth about her treatment of our government’s secrets.”

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