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The classified material included in the latest batch of Hillary Clinton emails flagged by an internal watchdog involved discussions of CIA drone strikes, which are among the worst kept secrets in Washington, senior U.S. officials briefed on the matter tell NBC News.

The officials say the emails included relatively “innocuous” conversations by State Department officials about the CIA drone program, which technically is considered a “Special Access Program” because officials are briefed on it only if they have a “need to know.”

As a legal matter, the U.S. government does not acknowledge that the CIA kills militants with drones. The fact that the CIA conducts drone strikes in Pakistan and Yemen, however, has long been known. Senior officials, including Sen. Dianne Feinstein and former CIA Director Leon Panetta, have publicly discussed CIA drones.

In 2009, Feinstein disclosed during a public hearing that the U.S. was flying Predator drones out of a base in Pakistan. Also that year, Panetta called drone strikes in Pakistan “the only game in town in terms of confronting or trying to disrupt the al Qaeda leadership.” Various public web sites continue to keep track of each CIA drone strike.

At issue are a new batch of emails from Clinton’s home server that have been flagged as containing classified information in a sworn statement to the inspector general of the intelligence community. The sworn statement came from the CIA, two U.S. officials tell NBC News.

In a letter to lawmakers first reported Tuesday by Fox News, the intelligence community’s inspector general said some of Clinton’s emails contained information classified Top Secret/Special Access Program, a secrecy designation that includes some of the most sensitive, most closely held U.S. intelligence matters.

The inspector general, Charles McCulllough said in a letter to the chairmen of the Senate intelligence and foreign affairs committees that investigators had found “several dozen emails containing classified information determined by the IC element to be at the CONFIDENTIAL, SECRET and TOP SECRET/SAP information.”

The letter doesn't make clear whether Clinton sent or received the emails in question, but in the past, emails containing classified information have tended to have been sent to Clinton, not written by her.

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On Tuesday, Sen. Feinstein, ranking Democrat on the intelligence committee, criticized the original Fox News story about the Inspector General’s letter as partisan, and said “none of the emails that are alleged to contain classified information were written by Secretary Clinton.”

“None of the emails that were sent to Secretary Clinton were marked as including classified information, a requirement when such information is transmitted,” said Feinstein, who is backing Clinton for the 2016 Democratic presidential nomination.

The description of the emails as relatively innocuous came from officials, including a senior U.S. intelligence official, who believe Inspector General McCullough has been unfair to Clinton in his handling of the issue. They say McCullough and Congressional Republicans have elevated a mundane dispute about classification into a scandal.

They point out that McCullough, a career intelligence official, contributed $1,000 to George W. Bush’s 2004 presidential campaign.

McCullough’s defenders note that he was appointed in 2011 by President Barack Obama. His office said he was not available for comment.

The emails in question are not the same two emails from Clinton’s server that have long been reported as containing information deemed Top Secret.

One of those involved a drone strike, and the other was related to North Korea. The State Department argues that the North Korea email, written by Kurt Campbell, then assistant secretary of state for East Asian and Pacific Affairs, was not classified because they say it was based on public sources, not intelligence information.

The term “special access program” is commonly associated with the military, but the inspector general’s latest letter used it to refer to the CIA drone program, officials said.

Clinton and State Department officials have repeatedly said that none of the information she sent or received while secretary of state was marked classified, and nothing has emerged to contradict that. But it’s become clear that classified information bled into the emails, which were sent over unencrypted channels open to interception by foreign intelligence agencies.

Clinton campaign spokesman Brian Fallon said the latest information about the emails makes it "absurd to suggest that Secretary Clinton did anything wrong."

He added, "Both the sending and the leaking of [the IG's] letter was a reckless and irresponsible act."

While she was secretary of state from 2009 to 2013, Clinton conducted government business over private email routed through a server she kept in her home in Westchester County, N.Y. When her use of the server was disclosed, it set off a chain of congressional inquiries and litigation that has dogged her presidential campaign.

The State Department is under court order to release Clinton’s government-related emails under the Freedom of Information Act. Clinton has turned over about 55,000 emails, and almost all have been released, though they have been heavily censored. The last batch is due to be made public Jan. 29.

-- Andrea Mitchell and Monica Alba contributed to this report.