Afghan Defense Ministry spokesman Zahir Azimi said the prisoners had been released from a detention facility near the Afghan capital, Kabul, and would be sent back to their respective home areas throughout Afghanistan.
The U.S. embassy in Kabul called it a "deeply regrettable" move that ran counter to a 2012 agreement on detainees.
"The Afghan government bears responsibility for the results of its decision," the embassy said in a statement on its website.
The U.S. military has said the men should be tried in Afghan courts.
A U.S. military official, speaking on condition of anonymity, said the United States had provided Afghan officials with "hundreds of pages" of evidence or investigative leads against the prisoners.
Some of the detainees, he claimed, had been linked by fingerprints or other evidence to the production or placement of improvised bombs.
The prisoners were transferred to Afghan authority last year as part of the U.S. and NATO transition out of Afghanistan.
The fate of another 23 prisoners who the United States contends should not be released is being examined by the Afghan government, the U.S. official said.
The detainees have become one more issue fuelling tension in U.S.-Afghan ties ahead of a presidential election in April and the planned pullout of most foreign troops by the end of the year.
The Obama administration has been pressing Afghan President Hamid Karzai for months to sign a bilateral security agreement with Washington that would allow some U.S. troops to stay beyond the end of this year.
NJF/NJF