There was a cover-up when it came to Hillary Clinton's use of a private email server, and the State Department "aided and abetted that cover-up," Rep. Trey Gowdy, who chairs the House's Select Committee on Benghazi, said Sunday.

Gowdy said that arrangement went on to allow Clinton to keep her emails for two more years after she left office.

"She had this arrangement for the entire time she was secretary of state, then she kept them for two years," the South Carolina Republican lawmaker told Fox News' Bret Baier. "It was only because the State Department would not go away, and that's when it gets interesting."

He said there were conversations between Clinton's former Chief of Staff Cheryl Mills, State Department Undersecretary for Management Patrick Kennedy, and Platte River Networks, the Colorado company that managed Hillary Clinton's emails after she left office, and after his committee sent out subpoenas, emails were destroyed.

"The State Department, which is supposed to be apolitical, non-interested in the next presidential election, has been covering for Hillary Clinton since she left office," said Gowdy.

On Friday, the FBI released yet another large trove of documents concerning the email server, including notes stating that an unnamed Platte River email said in 2014 email there was a "cover-up operation" going on with the former secretary's communications, reports The Daily Caller.

The Department of Justice has offered at least partial immunity, through the FBI, including to Mills, and Gowdy said that doesn't make sense to him.

"Number one, if you think that there is evidence that is relevant to an investigation on a piece of physical property, you use a subpoena, a grand jury subpoena," said Gowdy. "You don't strike an immunity agreement with the computer, you go get the computer. Her lawyer, Beth Wilkinson, who represents Heather Samuelsson and Cheryl Mills, she's on record of saying, 'The Department of Justice assured me my clients did nothing wrong.'

"Well, people who have done nothing wrong typically don't ask for immunity so my question would be immunity from what? What was it you were worried about?"

Gowdy said he thinks that's because Clinton "had classified information on those computers, so you offer immunity to Cheryl Mills, who has classified information on her computer. How can you possibly then prosecute Hillary Clinton for having classified information on her computer? You couldn't do it."

The congressman said he doesn't want to "malign the FBI," but at the same time, he has "been underwhelmed by an agency that I once had tremendous respect for. The Department of Justice gives out any immunity. The FBI doesn't immunize anyone."

Also, he pointed out that the DOJ is headed by Attorney General Loretta Lynch, who met on her private plane with former President Bill Clinton.

"[She] met on the tarmac for half an hour to discuss golf and grandkids with a potential witness, to say nothing about the spouse of a potential target, a potential witness in an investigation, she recuses herself?" said Gowdy.

"Someone in the Department of Justice had to decide to pass out these immunity agreements. I have seen the get out of jail free cards. What I don't see is the jail. Usually you strike immunity to further a prosecution. There is no prosecution. It's just five get-out-of-jail-free cards."

Political commentator Charles Krauthammer, appearing later on the show, said he thinks Gowdy is "absolutely right" with his claims.

"The more you look at these document dumps, the more you look at the things that were done, the granting of immunity, as Gowdy explained, there was no need for that," said Krauthammer.

"All you had to do was issue a subpoena and since it came from the Department of Justice . . . it was understood from the beginning by the Department of Justice and the White House, the legacy of the president was going to hang on her winning reelection and that there was no way they were going to prosecute her."

Further, said Krauthammer, he believes FBI Director James Comey was in a position where he did what he had to do.

"He's not a stupid man," said Krauthammer. "He understood that was the setting for the whole play and his job, I think that he failed, I'm imputing this to him, was to come out with his reputation reasonably intact by laying out the indictment without indicting. I don't know if that's a happy compromise but that looks to me what actually happened."