There are 158 prisoners on the Cuba base
They say this is to allow detention facilities to be added and upgraded.
The decision comes amid growing international criticism of the conditions under which al-Qaeda and Taleban suspects are being held at the base.
But a Pentagon official said criticism of the prisoners' treatment was "not a factor" in the decision.
On a visit to Afghanistan, the head of the American FBI, Robert Mueller, made an unannounced visit to the US military base in the southern city of Kandahar, where al-Qaeda and Taleban prisoners are being held.
He said the interrogation of the prisoners had prevented attacks against US targets around the world.
Temporary
There are 158 prisoners at Guantanamo at the moment, and US officials say they need to expand the facilities in order to increase the number housed there.
The BBC's Mike Fox said the halt is only going to last a few days, with building work likely to continue around the clock.
Officials say the temporary halt is not linked to the recent wave of criticism of the prisoners' treatment - the base simply cannot accomodate the several hundred prisoners still being held by the US military in Afghanistan.
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Washington believes that interrogating the men will yield invaluable information on the terror network led by Osama Bin Laden.
Visiting the base where prisoners are held in Kandahar, FBI Director Robert Mueller said questioning the suspects had already served a good purpose.
"Information we have picked up since the war has prevented additional attacks around the world," Mr Mueller said.
"Interrogations from al-Qaeda members detained here in Afghanistan as well as documents... have prevented additional attacks against US facilities around the world."
Criticism
Criticism of the US treatment of the Guantanamo prisoners grew after it emerged that they had been handcuffed, blindfolded and shackled during their transfer, and that they were being confined in open-sided wire cells. Some had been sedated on the flight from Afghanistan.
The US administration classifies the detainees as "illegal combatants" rather than prisoners of war, thereby denying them rights enshrined in the Geneva Convention on prisoners of war.
However, it insists they are being treated humanely.
On Tuesday, US Defence Secretary Donald Rumsfeld angrily rejected the criticism as "just plain false".
"What's going on down there is responsible, humane, legal, proper and consistent with the Geneva Convention," he said.
"I haven't found a single scrap of any kind of information that suggests that anyone has been treated anything other than humanely."
His comments came as US human rights advocates launched a legal challenge against the detention of the prisoners, saying it violated international law and the United States constitution.
The criticism has been spearheaded by human rights groups, including Amnesty International and the International Red Cross.
