Defence secretary Lloyd Austin on Friday overrode a plea agreement reached earlier this week for the accused mastermind of the September 11, 2001, attacks and two other defendants.
The cases have been reinstated as death penalty cases.
The move comes two days after the military commission at Guantanamo Bay, Cuba, announced it had reached plea deals with Khalid Sheikh Mohammed and two accused accomplices in the attacks.
Khalid Sheikh Mohammed and two accomplices, Walid Bin Attash and Mustafa al-Hawsawi, were expected to enter the pleas at the military commission at Guantanamo Bay, Cuba, as soon as next week.
FILE- Khalid Sheikh Mohammed, the alleged September 11 mastermind, is seen shortly after his capture during a raid in Pakistan Saturday March 1, 2003 (File/AP)
Pentagon officials declined to release the terms of the initial plea bargain.
The New York Times, citing unidentified Pentagon officials, said the terms included the men’s longstanding condition that they be spared risk of the death penalty.
Defence lawyers had requested the men receive life sentences in exchange for the guilty pleas, according to letters from the federal government received by relatives of some of the nearly 3,000 people killed outright on the morning of September 11.
The now-overridden US agreement with the men to enter into a plea agreement comes more than 16 years after their prosecution began for al Qaeda’s attack, and over 20 years after militants flew commandeered commercial airliners into buildings.
The attack killed nearly 3,000 people and triggered years of US wars against militant extremist groups that reshaped Middle Eastern countries.
Terry Strada, national chairwoman of a group of families of victims called 9/11 Families United, had been at Manhattan federal court for a hearing on one of many civil lawsuits when she heard news of the plea agreement.
She said many families just wanted to see the men admit guilt.
“For me personally, I wanted to see a trial,” she said. “And they just took away the justice I was expecting, a trial and the punishment.
“They were cowards when they planned the attack. And they’re cowards today.”
Dozens of relatives of those killed have died while awaiting resolution of the case, Ms Strada added.