The man accused of being the mastermind of the Sept. 11 attacks, Khalid Shaikh Mohammed, has agreed to let government prosecutors use portions of a 2007 confession that he says were obtained through his torture at any future sentencing trial if his case is settled with a life sentence.

Defense lawyers have been trying for years to have those confessions excluded from the death-penalty trial against Mr. Mohammed and three other men accused of plotting the Sept. 11, 2001. The lawyers had argued that he was conditioned to answer his captors’ questions in a secret C.I.A. prison network where he was waterboarded, beaten and subjected to rectal abuse.

But an excerpt from his plea deal that was released by a federal court over the weekend shows that Mr. Mohammed agreed that prosecutors can use certain portions of his disputed confessions against him at a sentencing trial — if he is allowed to plead guilty.

That deal is in the midst of a heated political and legal controversy that is spilling over into the Trump administration.

On July 31, after more than a decade of litigation, a senior Pentagon appointee signed separate agreements with Mr. Mohammed, Walid bin Attash and Mustafa al-Hawsawi to settle their capital case in exchange for their giving up the right to appeal their convictions and challenge certain evidence. Those deals were submitted to a military judge, under seal.

Then, two days later, Defense Secretary Lloyd J. Austin III moved to withdraw from the deals. He retroactively stripped his appointee, Susan K. Escallier, a retired Army lawyer, of the authority to reach the deal and said he wanted the men to face trial.