War court prosecutors are asking a military judge to refrain from taking guilty pleas from Khalid Shaikh Mohammed, who is accused of masterminding the Sept. 11 attacks, and from two men accused of conspiring with him until a higher court decides the validity of their plea agreements.

In separate notices to the court and to the families of the nearly 3,000 people who were killed in the attacks, prosecutors said on Friday night that the government had decided to appeal the judge’s decision earlier in the week to take the pleas.

Clayton G. Trivett Jr., the lead prosecutor, went further. He notified the judge’s legal adviser that he intended to ask the judge, Col. Matthew N. McCall, during a rare court hearing on Sunday to suspend preparations for guilty plea proceedings next week. If he refused, Mr. Trivett said, the government would ask the Pentagon’s appeals panel for the military commissions to impose a stay on the proceedings, so they could prepare a full appeal.

The development was the latest to whipsaw Sept. 11 family members, who have responded emotionally to the settlement that was reached on July 31, undone on Aug. 2 and reinstated this week.

The government’s decision to appeal means the question of whether Mr. Mohammed can plead guilty in exchange for a life sentence or whether he must face a full trial will probably not be decided in the dwindling days of the Biden administration.

At Guantánamo, the decision disappointed Maureen Basnicki, 73, a Canadian citizen whose husband, Kenneth, was killed at the World Trade Center. She had extended her stay into next week to watch the guilty plea proceedings.