The Pentagon chief was caught off guard by last week’s decision by prosecutors to offer deals to the men.
The US defence secretary has revoked plea deals with Khalid Sheikh Mohammed and two alleged accomplices.
Mohammed and two other defendants likely to enter formal plea next week over attacks that killed nearly 3,000 people.
Incompetency finding for Ramzi bin al-Shibh means the prosecution of his four co-defendants would continue without him.