The Bush administration has told the federal courts, with varying success, that judges have no jurisdiction over "enemy combatants" or detainees held at the U.S. naval base in Guantanamo Bay, Cuba.
None of the detainee cases has reached the Supreme Court.
Breyer's comments came in prepared remarks for a speech Monday before the Association of the Bar of the City of New York. Breyer is the Supreme Court's most junior member, but a leader of its liberal wing.
The justice said the detainees came in three categories: "The approximately 600 individuals from 42 different countries who fought against allied forces in Afghanistan and are presently detained at Guantanamo Bay ... two American citizens, accused of crimes related to terrorism, who have been detained in military prisons; and ... 200 of the thousand or so individuals arrested by the government after Sept. 11 (2001) who are still being detained. This group includes aliens illegally in the United States, material witnesses and a few individuals accused of terrorism-related crimes."
Without referring to the Bush administration's legal position, the justice said the security sweeps since the Sept. 11 terror attacks have raised a number of questions for the court.
"The detainees may ask the courts to decide, another other things: What law applies to the detainees in Cuba? ... Are the restrictions imposed upon the two American citizens detained in military prisons consistent with basic constitutional guarantees?"
A Saudi national born in Louisiana is being held in a Navy brig in South Carolina as an "enemy combatant" after being captured in Afghanistan.
Jose Padilla, born in Brooklyn, was arrested last May in Chicago as he tried to re-enter the country from Pakistan. Accused of plotting with al-Qaida to use a radioactive "dirty" bomb in a U.S. city, Padilla is also being held as an "enemy combatant" in a brig in Virginia while the government tries to fight his access to the courts or to a lawyer.
"What rights, if any, does the Constitution offer foreigners illegally present in the United States?" Breyer said in his speech. "What are the rights of material witnesses? In particular, to what extent and in what circumstances do ordinary courts lack jurisdictional competence to decide these questions?"
Breyer said he did not know how the courts would decide the questions, but the courts, not the government, would do the deciding.
If "the government claims that the court lacks jurisdiction to decide a particular matter, the court, not the government, will decide if that is so, with the result in a lower court being subject to appeal," eventually all the way to the Supreme Court, Breyer said.
The Constitution applies even in times of dire emergency, he added later.
Breyer said the federal courts should learn from mistakes made in the past.
Those mistakes included, he said, "the speech-censoring Alien and Sedition Acts ... during the Republic's early years ... President (Abraham) Lincoln's suspension of the writ of habeas corpus during the Civil War. As a result, Union generals imprisoned 13,000 to 18,000 people -- all without benefit of judicial process."
The mistakes also included the internment of Japanese-Americans during World War II, "when the federal government removed 110,000 individuals of Japanese origin, two-thirds of whom were American citizens, from their homes in California, sending them to camps ... in Mountain and Midwestern states."
Breyer said the internment occurred despite word from the FBI and then-Director J. Edgar Hoover "that they had no evidence of any act of sabotage or any sabotage threat."
The Supreme Court, in 1944's Korematsu vs. the United States, "a decision that we now recognize as shameful, held that the Constitution permitted it."