The man accused of plotting the attacks of Sept. 11 and two of his accomplices have agreed to plead guilty to conspiracy charges in exchange for a life sentence rather than a death-penalty trial at Guantánamo Bay, Cuba, prosecutors said Wednesday.

A senior Pentagon official approved the deal for Khalid Shaikh Mohammed, Walid bin Attash and Mustafa al-Hawsawi, according to Defense Department officials with knowledge of the agreement. The men have been in U.S. custody since 2003. But the case had become mired in more than a decade of pretrial proceedings that focused on the question of whether their torture in secret C.I.A. prisons had contaminated the evidence against them.

Word of the deal emerged in a letter from war court prosecutors to family members of victims of the attacks on Sept. 11, 2001.

“In exchange for the removal of the death penalty as a possible punishment, these three accused have agreed to plead guilty to all of the charged offenses, including the murder of the 2,976 people listed in the charge sheet,” said the letter, which was signed by Rear Adm. Aaron C. Rugh, the chief prosecutor for military commissions and three lawyers on his team.

The letter said the men could submit their pleas in open court as early as next week.

The plea averted what was envisioned as an eventual 12- to 18-month trial, or, alternatively, the possibility of the military judge throwing out confessions that were key to the government’s case. Col. Matthew N. McCall, the judge, had been hearing testimony this week and had more hearings scheduled for later this year to decide that and other key pretrial issues.