The military judge in the Sept. 11 case authorized lawyers on Wednesday to investigate whether Defense Secretary Lloyd J. Austin III lawfully rescinded a plea agreement with the man accused of planning the attacks, Khalid Shaikh Mohammed, and two accused accomplices.

In doing so, Col. Matthew N. McCall, the judge, declined a request by Mr. Mohammed’s lawyer to rule narrowly on whether Mr. Austin breached a lawful contract and, if so, hold a hearing this week on his plea.

The long-running case was thrown into confusion last week after a senior Pentagon official who oversees the military commissions signed an agreement with the three defendants to resolve the case with lifetime sentences — then, two days later, Mr. Austin rescinded it. Mr. Austin said they should face a death-penalty trial.

Colonel McCall ordered briefings on the question of whether there was unlawful influence in the case in time for the next round of hearings, starting on Sept. 16, days after the 23rd anniversary of the attacks that killed nearly 3,000 people. The plea agreements remain under seal as case evidence.

He also instructed the government to swiftly comply with requests by defense lawyers for information about the circumstances surrounding Mr. Austin’s decision.

“Everybody must follow the rules, including the secretary of defense,” Colonel McCall said. “I’m not going to rush,” he said, pledging not to be affected “if more political pressure is put on the parties.”