Afghanistan has enough evidence to try only 16 of 88 prisoners the US considers a security threat and plans to free the remaining detainees, the president's spokesman has said.
The move will further strain relations between the two countries, which are already near breaking point over President Hamid Karzai's refusal to sign a security deal to shape the US military presence after most foreign troops leave this year. Without a deal, Washington could pull most of its troops out next year.
America is strongly opposed to the release of the prisoners because it says they have been involved in the wounding or killing of US and coalition troops.
State Department spokeswoman Jen Psaki said the US considered 72 of the detainees dangerous. "These 72 detainees are dangerous criminals against whom there is strong evidence linking them to terror-related crimes, including the use of improvised explosive devices, the largest killer of Afghan civilians," she said.
Psaki said "time will tell" whether the release of the detainees would affect the signing of the agreement. She said it was in the interests of the Afghan people and the government to sign it.
But Kabul says there is no evidence against 45 of the 88 prisoners, while the evidence against a further 27 detainees is not sufficient to put them on trial.
"We cannot allow innocent Afghan citizens to be kept in detention for months and years without a trial for no reason at all," Karzai spokesman Aimal Faizi said. "We know that unfortunately this has been happening at Bagram, but it is illegal and a violation of Afghan sovereignty and we cannot allow this any more."
The president's decision came after the head of Afghanistan's spy agency presented the cases against the prisoners at a meeting on Thursday.
US senators visiting Afghanistan last week said releasing the prisoners would irreparably damage ties, but stopped short of saying it would prompt a full military withdrawal.
On Thursday, senators John McCain and Lindsey Graham said they had made clear to Karzai in Kabul last week their objections to the release, and said there could be some action in response.
"We are in contact with our military and civilian leaders in Afghanistan and will determine what course of action is appropriate once we have received additional information," the two Republicans said.