Roughly 1,000 emails between Hillary Clinton and Gen. David Petraeus were thought to be missing from the 30,000 emails provided by Clinton’s team to the State Department in December 2014, according to the newly released FBI investigative files.

Additional documents obtained through a federal lawsuit by Judicial Watch show Clinton had directed Petraeus to send her emails at her personal address, which was used for all government work during her tenure as secretary of state.

In a heavily redacted FBI interview summary from Aug. 17, 2015, a State Department employee from the Office of Information and Programs and Services (IPS), which handles Freedom of Information Act requests, discussed how Petraeus’ records apparently were not among the work-related emails provided by the former secretary's team.

"CENTCOM records shows approximately 1,000 work-related emails between Clinton's personal email and General David PETRAEUS, former Commander of CENTCOM and former Director of the CIA," said the employee, whose name is redacted, according to the summary. "Most of those 1,000 emails were not believed to be included in the 30,000 emails that IPS was reviewing. Out of the 30,000 emails, IPS only had a few emails from or related to PETRAEUS as well as a few related to Leon PANETTA, former Secretary of Defense."

The same employee reported on a January 2015 status briefing about the emails given by State Department senior official Patrick Kennedy who is now at the center of "quid pro quo" allegations – that he offered to help the FBI get more slots for agencies overseas in exchange for downgrading an email to unclassified. The FBI and State now emphasize the deal never happened.

"KENNEDY and [redacted] were each provided with two binders full of email examples of documents [redacted] believed were possibly classified. [Redacted] returned her binders to [redacted] but KENNEDY decided to keep his binders following the brief. [Redacted] was not aware of anyone in IPS or at STATE who received the rules or parameters the CLINTON team and/or WILLIAMS & Connolly used to segregate Clinton's personal and office work emails."

As previously reported by Fox News, there are still two missing “bankers boxes” of emails that cannot be accounted for by Hillary Clinton’s legal team Williams & Connolly.

Clinton later maintained during congressional testimony that her team read every email, but FBI Director James Comey later said that was not true and only broad search terms were used.

In addition, new emails obtained through an ongoing federal lawsuit by Judicial Watch show that on Jan. 10, 2009, Clinton told Petraeus -- who was then CENTCOM commander -- to use her personal address on a BlackBerry account. "If there is ever anything you need or want me to know, pls use this personal email address. All the best, Hillary," she wrote.

One of the most intriguing and highly redacted documents released by the FBI is a witness interview with a CIA agent on June 10, 2016. The names of the FBI agents and the CIA agent and attorney are all redacted, but it is clear they were reviewing “Top Secret” emails too damaging to national security to release under any circumstances.

According to page 66, “After reviewing the email, [redacted] exclaimed [redacted] is an idiot. [redacted] further explained he believed the email was problematic.” The CIA was apparently referring to the writer of the email, adding "[redacted] expressed his opinion that DoS was not very careful."

Fox News estimates at least 95 percent of the CIA agent’s three-page interview was blacked out. “[redacted] did not have any direct knowledge of DoS officials using unclassified or ‘barely classified’ channels [redacted] but he suspected it," the document says. The CIA statement concluded as follows: “[redacted] expressed his opinion that DoS (Department of State) was not very careful [redacted].”

The CIA used the B(1) FOIA redaction 20 times. According to Freedom of Information Act exemptions, these redactions can include information about national defense, foreign policy, U.S. national security, transnational terrorism and sources or methods, or cryptology.

B(3) was used 25 times. This FOIA category redaction category prevents disclosure by statute which includes information about arms export control, immigration and Iran.

B(7) was cited for redactions three times. This FOIA category includes protected information about investigation techniques and personal privacy.

It is of note that this CIA agent was interviewed on June 10, just three weeks before Comey held his controversial press conference declaring that Clinton was not criminal but “extremely careless” in her handling of classified materials which included SAP content known as Special Access Programs or ‘above top secret.’

State Department Spokesperson John Kirby told Fox News:

“We can’t speculate about records that DOD may have. Nor can we verify the veracity of rumors. We can only speak to the records in our possession. As we disclosed last September, the State Department received from the Department of Defense and the State Inspector General several copies of a single email chain between former Secretary Clinton and then-Commander of US Central Command David Petraeus which were not previously in the possession of the Department. These emails are now in our possession and will be subject to Freedom of Information Act requests. Beyond that, our focus is on processing the material turned over by the FBI to comply with FOIA requests.”