This is just being reported by the Associated Press.
Here's more from the AP:
But The Associated Press has learned seven email chains are being withheld in full because they contain information deemed to be "top secret." The 37 pages include messages recently described by a key intelligence official as concerning so-called "special access programs" — a highly restricted subset of classified material that could point to confidential sources or clandestine programs like drone strikes or government eavesdropping.
Department officials wouldn't describe the substance of the emails, or say if Clinton sent any herself. They also wouldn't disclose if any of the documents reflected information that was classified at the time of transmission, but indicated that the agency's Diplomatic Security and Intelligence and Research bureaus have begun looking into that question.
Hillary Clinton used a private server for her entire term as Secretary of State. She transmitted classified and top secret information to and from that address. 22 of the e-mails that the government does have are clearly top secret. This will have big implications for Clinton, who is seeking the Democratic nomination for president.
Earlier this week, it was reported that the FBI could be close to an indictment of Clinton, though the agency has revealed little about the extend of their probe into the e-mail setup.