The judge refused to recuse himself from the trial of the alleged Al-Qaeda operative accused of masterminding the 2000 suicide attack on the USS Cole.
Abd al-Rahim al-Nashiri faces the death penalty over the bombing of the US Navy destroyer off Yemen in October 2000 that killed 17 sailors and an attack two year later that killed one person on the French oil tanker MV Limburg.
Al-Qaeda claimed responsibility for the suicide attack on the USS Cole, which saw militants riding an explosives-laden skiff blow a 30-by-30-foot (10-by-10-meter) hole in the ship.
Nashiri's lawyers had called on Judge James Pohl to recuse himself from the Guantanamo military tribunal trying the case, pointing to a judicial and financial conflict of interest.
But at a pre-trial hearing on Tuesday, Pohl -- the longest-serving judge in the US military -- said his impartiality could not be questioned and refused to stand down.
Pohl was slated to retire on October 1, 2010, after 30 years of service, but continues to work on "special status" renewed each year with a monthly salary of $10,557, according to the Pentagon.
He is currently the only judge serving at Guantanamo and has assigned himself to the proceedings against Nashiri and five men suspected over the September 11, 2001 attacks, as well as those against Pakistani Majid Khan, who has agreed to testify against other "high value" detainees.
He also oversaw certain trials against US military members accused of mistreating Iraqi prisoners at the Abu Ghraib jail.
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Nashiri's defense lawyer Richard Kammen argued unsuccessfully that because Pohl was on retirement recall status that could be terminated every year, he had a financial incentive to rule in favor of the military bureaucracy.
History will judge the decisions made at the proceedings, Kammen said, stressing that they represent the first military commission since reforms by the Obama administration in 2009.
"We don't know whether your future depends on a phone call," the lawyer told the pre-trial hearing.
Visibly irritated, Pohl referenced his 32 years of service -- including 12 as a judge -- adding that none of the arguments raised by the defense had merit.
Pohl added that he was serving at the pleasure of the army and not of military commissions.
Moving onto another request by the defense, the judge authorized that a picture of the suspect could be taken and sent to his parents and others. However, he refused to allow a video filmed in Saudi Arabia by the suspect's parents to be given to him.
Speaking in Pohl's defense, prosecutor Andrea Lockhart said the defense had not articulated any legal reasons for his recusal.
"A reasonable person knowing all the facts would not question the judge's partiality," she said.
Nashiri's trial could start as early as November, making it the first to take place at Guantanamo since the reform of military tribunals by the Obama administration in 2009.