An Afghan supreme court official had said earlier that the men were released from the US naval base at Guantanamo Bay in Cuba. But the chief justice said on Sunday the suspects never left Afghanistan.
"They have been released from Bagram," Chief Justice Fazl Hadi Shinwari said. "We will give them clothes and then send them home."
He said US authorities had said they would free their remaining Afghan prisoners.
"There are another 400 Taliban in Bagram and they [the US military] have promised to release all Taliban from Bagram and Guantanamo Bay," he said.
US forces captured hundreds of prisoners when they toppled Afghanistan's Taliban government in late 2001 for failing to surrender al-Qaida leader Usama bin Ladin.
Prisoners deemed to be the greatest security risk were taken, bound and shackled, to Guantanamo Bay while others were kept at US bases across Afghanistan.
Accusations of mistreatment of prisoners have dogged US military jails from Iraq, to Afghanistan and its base in Cuba.
"All the prisoners
under the custody
of the Americans,
either inside or outside Afghanistan, they are innocent people,
they are not Taliban"
Abdul Latif Hakimi,
"I have very bad memories of the interrogation because they were torturing us," Abdul Manan, 35, from Kunar, in eastern Afghanistan, said.
Manan was among the prisoners released on Sunday.
"But after the interrogation period was over, everything was all right," he said outside the Supreme Court in Kabul.
A Taliban spokesman said all Afghan prisoners should be freed.
"All the prisoners under the custody of the Americans, either inside or outside Afghanistan, they are innocent people, they are not Taliban," Taliban spokesman Abdul Latif Hakimi said by satellite telephone.
"The Americans are torturing and harming those innocent people in their jails."
About 18,000 US troops still are based in Afghanistan, engaged in the hunt for al-Qaida and Taliban remnants.