Judge James Pohl's ruling throws a wrench in President Obama's plans to suspend the military tribunal process for 120 days while the administration reviews how to close the Guantanamo Bay detention facility within the year.
Pohl's decision is striking because two other military judges in a Sept. 11 conspiracy case and in the case of Canadian Al Qaeda operative Omar Khadr agreed to suspend proceedings in accordance with Obama's recent executive order, which put a hold on all military tribunals.
Pentagon spokesman Geoff Morrell said Thursday that Pohl would soon be told to comply with Obama's executive order.
"All I can really tell you is that this department will be in full compliance with the president's executive order," Morrell said at a news briefing. "There is no ifs, ands or buts about that."
"The president has signed an executive order and that sort of puts all this on hold as we go about and review a number of things related to Gitmo, our detention operations, our interrogation procedures," he continued.
"And so, while that executive order is in force and effect, trust me that there will be no proceedings continuing down at Gitmo with military commissions," he added.
Al-Nashiri's arraignment is scheduled for Feb. 9 at Guantanamo Bay. A Defense Department spokesman said the only thing now that can stop the court appearance from going forward is a withdrawal of the charges without prejudice by Judge Susan Crawford, head of the convening authority that oversees the entire process at Guantanamo.
If the charges are dropped without prejudice, new charges could be brought in another venue, possibly a military court martial or criminal court.
The October 2000 attack on the USS Cole killed 17 service members and injured 50 others.
FOX News' Catherine Herridge contributed to this report.