The cases against the defendants have been bogged down in pre-trial manoeuvrings for years while the accused remained held at the Guantanamo Bay military base in Cuba.
Much of the legal jousting surrounding the men’s cases has focused on whether they could be tried fairly after having undergone methodical torture at the hands of the CIA in the years after Sept. 11.
Some families of the attack’s victims condemned the deal for cutting off any possibility of full trials and possible death penalties.
Republicans were quick to fault the Biden administration for the deal, although the White House said after it was announced it had no knowledge of it.
Republican Sen. Tom Cotton of Arkansas, a member of the Armed Services Committee, earlier on Friday had condemned the plea deal on social media as “disgraceful”. Mr Cotton said he had introduced legislation that would mandate the defendants face trial and the possibility of the death penalty.
Mohammed, whom the US describes as the main plotter of the attack that crashed hijacked passenger planes into the World Trade Center, the Pentagon and a Pennsylvania field, and the other two defendants had been expected to formally enter their pleas under the deal as soon as next week.
The US military commission overseeing the cases of five defendants in the Sept. 11 attacks has been stuck in pre-trial hearings and other preliminary court action since 2008. The torture that the defendants underwent while in CIA custody has been among the challenges slowing the cases, and left the prospect of full trials and verdicts still uncertain, in part because of the inadmissibility of evidence linked to the torture.
J. Wells Dixon, a staff attorney at the Center for Constitutional Rights who has represented defendants at Guantanamo as well as other detainees there who have been cleared of any wrongdoing, had welcomed the plea bargains as the only feasible way to resolve the long-stalled and legally fraught Sept. 11 cases.
Me Dixon accused Mr Austin on Friday of “bowing to political pressure and pushing some victim family members over an emotional cliff” by rescinding the plea deals.
Lawyers for the two sides have been exploring a negotiated resolution to the case for about 1.5 years.
President Joe Biden blocked an earlier proposed plea bargain in the case last year, when he refused to offer requested presidential guarantees that the men would be spared solitary confinement and provided trauma care for the torture they underwent while in CIA custody.
A fourth Sept. 11 defendant at Guantanamo had been still negotiating on a possible plea agreement.
The military commission last year ruled the fifth defendant mentally unfit to stand trial. A military medical panel cited post-traumatic stress disorder and psychosis, and linked it to torture and solitary confinement in four years in CIA custody before transfer to Guantanamo.