The Bush administration has suffered two legal setbacks in its efforts to curtail the rights of those it accuses of being involved in terrorism.
About 660 people are being held at the base in Guantanamo Bay
A federal appeals court has ruled US authorities do not have the power to detain a US citizen seized on US soil as an "enemy combatant".
And a court said detainees being held by the US military at Guantanamo Bay in Cuba should have access to lawyers.
However, analysts say both rulings could be overturned by higher courts.
The first decision, from an appeal court in New York, ruled that Jose Padilla - a US citizen arrested at Chicago airport and accused of being involved in a plot to set off a radiological weapon - cannot be held indefinitely in a military prison.
Mr Padilla has been held in a naval facility in Charleston, South Carolina, since June 2002 as an enemy combatant following a presidential decree.
Jose Padilla is currently being held in a military jail
Mr Padilla is thought to be the only US citizen since World War II to be detained on a presidential order.
The court said that, although it recognised that the US Government had a responsibility to protect the nation, presidential authority "does not exist in a vacuum".
The judges said Mr Padilla should be released from military custody, but added that the US Government was free to transfer him to civilian jurisdiction.
White House spokesman Scott McClellan called the court's ruling "troubling and flawed" and said the US Justice Department would seek a stay on the court's ruling and request further judicial review.
The decision came shortly after another US federal appeals court in San Francisco, California, ruled that detainees being held by the US military at Camp Delta in Guantanamo Bay, Cuba should have access to lawyers and US courts.
The Guantanamo ruling - relating to the case of a Libyan national captured in Afghanistan - is the first to overrule the US administration's position that the men held there can be detained indefinitely without legal recourse.
"Even in times of national emergency... it is the obligation of the judicial branch to ensure the preservation of our constitutional values and to prevent the executive branch from running roughshod over the rights of citizens and aliens alike," the 2-1 ruling by the Ninth Circuit Court of Appeals said.
The issue of representation in US courts for Guantanamo detainees is already under investigation by the nation's highest legal body, the US Supreme Court.
BBC correspondent Justin Webb in Washington says this judgement from a court known for its hostility to the Bush administration will probably not take effect until the Court rules next year on the issue and it could be overturned.
But it does set the stage for the possibility that the US legal profession will force legal representation and legal rights to be given to Guantanamo prisoners, our correspondent adds.
'Reminder to Bush'
Human rights organisations welcomed the rulings.
"[The decision] should serve as a further reminder to the Bush administration that the practice of indefinite detention without charge or trial is wrong and should be
repudiated at home as it is abroad," Vienna Colucci from Amnesty International USA said.
The ruling on Mr Padilla's case came as US prosecutors said a Briton being held in the US on suspicion of trying to sell anti-aircraft missiles will face new charges of plotting to obtain a dirty bomb.
Hemant Lakhani, 68, has also been charged in New Jersey with offering to obtain tanks and armoured personnel carriers, they said.