Another military source supported this account, telling Fox News that all signs in recent weeks point in that direction.
Asked to respond to claims that the commissions were told to stand down, a senior administration official told Fox News, “we intend to use all of the tools at our disposal to bring these guys to justice.”
In July, sources told Fox News that the Obama administration was holding off on a public decision on which venue would be used to try the Sept. 11 terror suspects until after the midterm elections.
The administration was reluctant to send the trials back to military commissions or hold the alleged 9/11 conspirators indefinitely under the laws of war because it would further alienate the president’s supporters on the left, sources told Fox News.
Liberals have expressed disappointment that the administration has apparently backed off of Attorney General Eric Holder’s decision last November to prosecute the suspects as criminals in a New York federal court.
The Washington Post reported earlier this month that the administration was now considering indefinite detention for the men.
The chief prosecutor for the military commissions, Cpt. John Murphy, told Fox News that his office is actively prepping between 50 and 60 cases, including the 9/11 case, and he was adamant that no order to halt their work has been given.
"No one at the White House has told us to stand down or to disband," he said.
Murphy would not discuss the details of a meeting last week between himself and Defense Department General Counsel Jeh Johnson after the verdict in the Ahmed Ghailani case except to say that it did not involve disbanding the commission office.
Ghailani was the first Guantanamo Bay detainee to stand trial in federal court who was subject to the CIA’s enhanced interrogation. Ghailani was accused of conspiracy and murder in the bombings of the U.S. embassies in East African in 1998. U.S. officials say Ghailani was not one of the three detainees who was waterboarded by the CIA.
Sources told Fox News the meeting between Murphy and Johnson was to discuss the impact of the Ghailani verdict as well as “future staffing issues.” Ghailani was convicted on only one of 285 counts by the jury – conspiracy to destroy government property and not murder.
Though the attorney general announced in November 2009 that the USS Cole case would be prosecuted by a military commission, no charges have been referred a year later. Abd al-Rahim al-Nashiri is accused of coordinating the suicide attack that struck the Navy vessel off the coast of Yemen in October 2000, killing 17 sailors.
Murphy said the commissions could not move forward on the cases until Defense Secretary Robert Gates removed an important block.
"OMC has no authority to refer charges on the USS Cole case and others because the order by the Secretary of Defense in early 2009 is still in place,” Murphy added. “We will not refer charges until the order has been lifted."
In January, the military charges against the five 9/11 suspects were withdrawn without prejudice by the Defense Department. Sources told Fox News at the time it was an effort to preserve the military’s legal position in case the men were not prosecuted in federal court as the attorney general announced and the case went back to Guantanamo.
The decision to pull the charges and the failure to move the case to a federal court means that no one is now charged with the murder of nearly 3,000 Americans -- and there is no public timetable for when the case will move forward.
Catherine Herridge is an award-winning Chief Intelligence correspondent for FOX News Channel (FNC) based in Washington, D.C. She covers intelligence, the Justice Department and the Department of Homeland Security. Herridge joined FNC in 1996 as a London-based correspondent.