Military judge hands down controversial plea deals involving 9/11 terrorist Khalid Sheikh Mohammed and two co-defendants back on the table, defying an order by Defense Secretary Lloyd J. Austin earlier this year.

An unnamed official told The Associated Press on Wednesday that the decision to restore the deals was made by Air Force Col. and Judge Matthew McCall. The US military has not yet announced the decision.

The plea deals in long term case against terrorists were struck earlier this summer. The defendants are incarcerated in Guantanamo Bay, Cuba, and the deals were approved by the top military Gitmo commission official.

If the plea negotiations are completed, Khalid Sheikh Mohammed – suspected to be the main architect of The September 11 attacks – and two co-defendants would avoid the death penalty in exchange for guilty pleas.

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A judge recently issued an order upholding a plea deal involving Khalid Sheikh Mohammed. (Getty Images)

The plea deals were condemned by a number of 9/11 victims and US politicians. The Pentagon revoked the agreements in July.

“Effective immediately, in exercise of my authority, I am withdrawing from the three preliminary agreements you signed on July 31, 2024,” a letter from Austin said.

The Biden administration distanced itself from the accords. In July, Pentagon officials said Austin was surprised by news of the deals.

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Khalid Shaikh Mohammed, a suspected al Qaeda terrorist, is pictured in this photo released by the FBI on October 10, 2001 in Washington, DC Mohammed was arrested at a home in Rawalpindi, Pakistan. (Getty Images)

“This is not something the secretary has been consulted about,” Pentagon press secretary Sabrina Singh said at the time. “I didn’t know that the prosecution or the defense would enter into the terms of the plea agreement.”

Terry Strada, the national president of 9/11 Families United, denounced the plea negotiations to Fox News Digital earlier this year.

“(The terrorists) committed this heinous crime against the United States,” Strada said. “He should have faced the charges, faced the trial and faced the punishment. Since when can people guilty of murder set fires?”

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Fox News Digital has reached out to the Pentagon for comment.

Fox News Digital’s Louis Casiano and The Associated Press contributed to this report.