In written arguments filed with the US Court of Appeals for the District of Columbia Circuit, the lawyers challenged the military's authority to arrest people overseas and detain them indefinitely without allowing them access to US courts to contest their detention.
Mr Bush gave the military that authority earlier this month when he signed a new law that sets up military commissions to hold trials for foreigners designated as "enemy combatants."
He hailed the law as a crucial tool in the war on terrorism and said it would allow prosecution of several high-level terror suspects.
Lawyers for more than 100 detainees who will be locked out of the court system under the new law asked the appeals court to let them to keep their legal challenge going in civilian courts.
They said that the creators of the US Constitution never would have permitted the government to hold people indefinitely without charging them.
"Persons imprisoned without charge must retain the right to obtain a court inquiry into the factual and legal bases for their imprisonment," lawyers wrote.
This argument echoes a Supreme Court ruling in June, when justices declared that the Bush administration's system of trying enemy combatants violated US and international law.
Within weeks, the president convinced Congress to pass a new law setting up military commissions and barring detainees from using the civilian court system.
Shortly after the new military commissions law was signed, the Justice Department told hundreds of detainees that their cases in the US courts had been rendered moot.
Seven retired federal judges from both the Republican and Democratic parties today filed legal briefs in the detainees case before the Washington appeals court, arguing that the military commissions law would allow authorities to use evidence obtained by torture.
Although the law prohibits torture, the judges said the military has not addressed torture claims made by detainees. The judges also argued that the new law illegally strips courts of the power to question military decisions about the detainees' torture claims.
The Justice Department has until November 13 to respond to the detainees claims.