Vaughn Ary, left, then staff judge advocate to the Marine Corps commandant, appears before Congress in June 2013. Ary, now retired, is stepping down as the convening authority for the military commissions at Guantanamo Bay, Cuba. (Douglas Graham/CQ Roll Call)

A senior Pentagon official overseeing the military tribunals at Guantanamo Bay, Cuba, is stepping down following a controversial order, now reversed, that would have required judges to relocate to the military base during the slow-moving process of trying detainees there.

Vaughn Ary, a retired Marine Corps major general who was appointed to a three-year term as the convening authority for the military commissions last fall, will resign effective Saturday, the Pentagon said in a statement.

Defense Secretary Ashton B. Carter selected Paul L. Oostburg Sanz, general counsel for the Department of the Navy, to fill the role on an interim basis.

Ary’s resignation comes several weeks after a military judge found that he had overstepped his authority and appeared to be trying to exert “unlawful influence” over cases moving toward trial at Guantanamo.

At issue was a decision this year by Deputy Defense Secretary Robert O. Work, who ordered that military judges overseeing trials of defendants charged in the Sept. 11, 2001, attacks and other cases should relocate to Guantanamo. He was following Ary’s recommendation to do so. Currently, judges spend part of each month at the military base, located on an isolated corner of Cuba.

“I believe the status quo does not support the pace of litigation necessary to bring these cases to a just conclusion,” Ary wrote to Work, the Pentagon’s No. 2 official, prior to the January order, according to a tribunal transcript.

The slow speed at which military trials are proceeding at Guantanamo is just one of the challenges facing the commissions. The system has been plagued by other controversies, including an FBI inquiry and the appearance of an interpreter who may have been present at CIA “black sites” overseas where some detainees were tortured.

Of the 122 detainees remaining at Guantanamo, 10, including those accused in the 9/11 attacks, are at some stage of a military trial. Others held at the detention center are awaiting transfer home or to third countries, while some are expected to be held indefinitely without trial.

President Obama has said he has not abandoned his goal of shutting down the prison, which is expensive to operate and remains a symbol of U.S. mistreatment of prisoners in the years after the 9/11 attacks. But he faces strong opposition in Congress to bringing detainees to the United States for trial and, in some cases, sending them to other countries.

While Ary had hoped to accelerate the trial process, defense attorneys argued that the order was an improper attempt to rush justice. This month, a military judge seemed to agree.

“There is no doubt the action of the convening authority and his legal advisers at a minimum appeared to attempt to unlawfully influence the military judge in this proceeding,” said Air Force Col. Vance Spath, who oversees a case against Abd al-Rahim al-Nashiri, a Saudi man accused in the 2000 USS Cole bombing. On March 2, Spath announced that Ary and his staff would be disqualified from involvement in that case.

Another judge ordered a pause to proceedings related to the 9/11 attacks because of the relocation plan. In late February, facing a backlash from military judges, Work rescinded the order.

“While the desire to speed up this process is understandable, Mr. Ary failed to recognize that this untested system that values secrecy more than efficiency simply cannot move quickly,” said Richard Kammen, lead counsel for Nashiri’s defense team.

“Only moving these cases to federal court will advance the goal of swift, fair trials whose results are likely withstand appellate review.”

Lt. Cmdr. Courtney Hillson, a Pentagon spokeswoman, said that Work had made the decision to rescind the order in response to the judge’s belief that it created an “inappropriate perception.”

“Work believes it is important to preserve the independence of the Military Commission in appearance, as well as in fact,” she said.

Adam Goldman contributed to this report.