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WASHINGTON — The emails on Hillary Clinton’s private server contained classified intelligence from some of the U.S. intelligence community’s most secretive programs, according to a new report.

The Intelligence Community Inspector General I. Charles McCullough III sent a letter to leaders on congressional intelligence committees last week detailing the findings from a review of Clinton’s emails, a spokeswoman for the inspector general confirmed to CNN.

Two government agencies flagged emails on Clinton’s server as containing classified information, the inspector general said, including some on “special access programs,” which are above “top secret” in classification level.

Clinton’s spokesman, Brian Fallon, appeared on CNN Wednesday morning to dispute the report. He argued on “New Day” that the information described as “classified” may be no more than a news article that was forwarded, although he ceded it is not entirely clear what classified material the report mentions.

Fallon argued that the crux of the issue is a dispute between the State Department and the intelligence community over what should be classified. He said the emails were not classified in the eyes of the State Department when they were sent to Clinton. Fallon also implied the inspector general has an ax to grind with Clinton.

There were several dozen emails in question beyond the two previously reported emails containing top secret information, according to the report.

Clinton’s campaign and the State Department have denied that any information was handled improperly, saying that the information and emails in question were all retroactively classified.

State also has noted that the same information can come from multiple sources, not all of which are classified.

State Department spokesman John Kirby said the department is still undergoing its review process, but any upgraded classification that is needed will be done.

“The State Department is focused on and committed to releasing former Secretary Clinton’s emails in a manner that protects sensitive information,” Kirby said in a statement. “No one takes this more seriously than we do. We have said repeatedly that we anticipate more upgrades throughout our release process. Our (Freedom of Information Act) review process is still ongoing. Once that process is complete, if it is determined that information should be classified as Top Secret, we will do so.”

The Justice Department is investigating if classified information improperly ended up on Clinton’s email server. The server contained correspondence between Clinton and a variety of aides and friends.

Republican lawmakers requested the inspector general investigate in March.

The Inspector General report was first reported by Fox News. It comes as the State Department is facing over a dozen Freedom of Information Act lawsuits related to information on or about Clinton’s private email server.

On Wednesday, the department released a set of emails between top Clinton aides and an IT staffer to The Daily Caller and the advocacy group Cause of Action in one such suit.

Earlier in the week, the same plaintiffs received emails from Clinton aide Huma Abedin, now a top official on Clinton’s presidential campaign, which show Clinton was given the option of using a State Department Blackberry for email purposes, but the option was dismissed.