Moreover, the Navy veteran said that the Bush administration's pick-and-choose application of the Geneva Conventions here could put American troops at risk.
"The government has asserted a position starkly different from the positions and behavior of the United States in previous conflicts, " he wrote, "one that can only weaken the United States' own ability to demand application of the Geneva Conventions to Americans captured during armed conflicts abroad."
The judge was acting on a petition brought by Hamdan, a single captive among the 550 so-called enemy combatants from 42 nations held for nearly three years.
A Yemeni who worked as bin Laden's $200-a-month driver on the al Qaeda mastermind's Kandahar farm, Hamdan denies being either a terrorist or an al Qaeda member.
He has said through his attorney that, if he can't go home, he wants to face charges in U.S. civilian court or through a military court-martial.
But the ruling clearly had sweeping consequences, given both the Justice Department's reply and interpretations by civil liberties and human rights lawyers.
"The spirit of it potentially extends more broadly to perhaps everything that is going on here at Guantánamo Bay, " said Neil Katyal, a Georgetown University law professor who sued on behalf of Hamdan in federal court and was co-defense counsel at Monday's hearing.
"It's a huge day for the Geneva Conventions, " said Human Rights Watch attorney Wendy Patten, adding the ruling "affirms that the president can't just declare people enemy combatants."
In addition, she said, the decision should end the U.S. government's reliance on World War II era case law, decided before the 1949 Geneva Conventions.
The three-member Military Commission panel made up of three colonels, two without any previous legal experience, suspended all its activities to study the ruling.
They had yet to decide whether they would continue writing decisions on a range of motions brought last week by attorneys for Australian David Hicks, who like the Hamdan team has filed a series of motions here challenging the war crimes court's legitimacy.