Then-Secretary of State Hillary Clinton had detailed knowledge about the security vulnerabilities involved in continuing to use her personal email despite claims that she didn’t really "stop and think" about the email system she was planning to use, newly released State Department emails show.

The new batch of emails also show three more exchanges containing classified information, according to Judicial Watch, a watchdog group that obtained the emails through a Freedom of Information Act lawsuit.

Justin Cooper, an aide to former President Bill Clinton, warned in 2011 about "overseas" use and other security issues concerning her emails and her personal BlackBerrys.

"All of your older messages will remain on the server. There is a way for me to move everything on to the new device, but the security whizzes have convinced me that this is a horrible thing to do because you also transfer any viruses, spyware and junk overseas providers hide on there," he told Hillary Clinton in an email dated June 6, 2011.

He went on to inform Clinton that he was planning to apply some new "security features and policies" on her new Blackberry, including a "more complex password."

"It is a constant fight to keep up with the security measures and unfortunately we keep seeing reminders of why we need to," he wrote.

Cooper is the Bill Clinton aide who asked State Department information technology specialist Bryan Pagliano to set up the private email server for Hillary Clinton in early 2009 when she started her job as secretary of state.

The Department of Justice in early January reportedly reopened an investigation into Clinton's use of a private email server. The probe is focused on how much classified information she exchanged or received on her private email server and whether top aides or Clinton herself was at fault for mishandling the information.

Clinton told NBC News in 2015 that she wished she had "made a different choice" when considering using an unsecured server but she was not "thinking a lot when I got in."

"You know, I was not thinking a lot when I got in," he said. "There was so much work to be done. We had so many problems around the world. I didn’t really stop and think, ‘What kind of email system will there be?'"

The Washington Post hours later reported that she had used personal funds to pay a State Department staffer to maintain the private email server, which she used for both personal and government matters.

Three other emails the State Department released this week demonstrate she was kept apprised of a wide variety of issues involving her use of a personal server.

A Sept. 29, 2009 email exchange between Cooper and Clinton discussed the backup of emails.

An Aug. 31, 2011 email between Cooper and Hillary Clinton discussed setting up Clinton's iPad and email interfaces with it.

A March 8, 2012 email exchange between Cooper, Pagliano, and Clinton with the subject line "Help!" discusses the "security landscape" differences between iPad, iPhone and blackberries. Clinton initiated the email expressing frustration that she is having blackberry "trouble" with her emails and receiving replies to emails she sends on blackberry only on her iPad.

"These new emails refute Hillary Clinton’s repeated claims of having little or no knowledge about her email system," Judicial Watch Tom Fitton said. "She clearly was fully in charge of setting up her outlaw email system and overseeing its use. When will the Justice Department act?"

The new batch of emails also show that Hillary Clinton sent classified information regarding Bahrain to Cooper, who reportedly lacked a security clearance. Hillary Clinton was instructing Cooper to show the Bahrain-related email to Bill Clinton.

"Just told my husband that the oppo in Bahrain posted on their website that they met [with] the #2 in our embassy who told them that the US supported them and their demands which was very upsetting to everyone. What's the story?" Clinton wrote to Jeffrey Feltman, the assistant secretary of the State Department's Bureau of Near Eastern Affairs, in a March 8, 2011 email.

Feltman responded that a "break-away part of the opposition did a sit-in outside the embassy and presented a petition."

"A political office (not #2) received the petition, as is customary, and urged the opposition to begin the dialogue," he said. "The petitioners then gave a false story about what our person said."

Clinton then forwarded the email to Cooper with a note to "Pls show to Bill from the bottom up. It responds to a question he just asked me."

On Feb. 13, 2010, Hillary Clinton passed along classified information to Cooper that U.S. Ambassador to Mexico Carlos Pascual sent to her chief of staff Cheryl Mills. The classified information included a note from Mexican Foreign Secretary Patricia Espinosa to Hillary Clinton.

Hillary Clinton tells Cooper to "pls look for Espinosa's note and respond. Thx."

In an Aug. 24, 2010 email, Clinton emailed Cooper classified information to print, including her "call sheet" for Indian Finance Minister Pranab Mukherjee.

Judicial Watch released the new emails and documents after the State Department provided them as part of its lawsuit. U.S. District Court Judge James Boasberg ordered State to produce all of the remaining 72,000 emails pages the FBI recovered in its investigation into Clinton's personal email server. The new batch of emails the court provided appear to be among those that Clinton previously had attempted to delete or failed to disclose, the watchdog said.

Until the court intervened, the State Department had been slow-walking the release of the documents at a rate that would have required Judicial Watch and the public to wait until at least 2020 to view all the Clinton material that is supposed to be publicly obtainable under FOIA law, Fitton said.

"The fact that Hillary Clinton and her agents tried to destroy or hide emails shows how she flagrantly and knowingly violated the laws that protect classified information and government records," Fitton said.