Citing his 26 years working in the regular court-martial system, he also described himself as “shaken” by the experience and portrayed Mr. Nashiri’s onetime defense lawyers as pursuing a “revolution to the system” by defying judicial orders.

Earlier this week, he had weighed having United States marshals seize two of Mr. Nashiri’s former lawyers — both civilian employees of the Pentagon — to force them to appear by video link from Virginia after they failed to comply with subpoenas, but decided against it.

On Friday, he argued that in his efforts to get Mr. Nashiri’s defense lawyers back to work on the case, “I’m not ordering the Third Reich to engage in genocide — this isn’t My Lai.” And he said he was weighing imminent retirement.

The latest trouble began in June, when Mr. Nashiri’s defense team discovered something in a room where they talked with their client. The details remain classified, but after Colonel Spath rejected the notion that there was a problem and tried to proceed, the civilians on Mr. Nashiri’s defense team quit in October, saying they had an ethical conflict.

That left only a junior, uniformed defense lawyer, Lt. Alaric Piette of the Navy. Lieutenant Piette has continued to appear in court but has not participated, arguing that he was unqualified and that the presence of a “learned counsel,” or death penalty specialist, is necessary — a contention Colonel Spath rejected.

Colonel Spath in November declared Brig. Gen. John Baker, who oversees military commissions defense lawyers, in contempt of court for refusing to order the two civilian Pentagon employees to resume work on the case. The general argued that he had the authority to dismiss them without the judge’s consent — another contention Colonel Spath rejected.

Colonel Spath ordered General Baker confined to a trailer and fined him, but after several days, Harvey Rishikof, a former civilian Pentagon official who was then the so-called convening authority overseeing the commissions system, freed the general and overturned the fine, although he left the contempt finding in place.