The handover of the controversial high security prison, sometimes referred to as "the other Guantanamo", had been hailed a victory for Afghan sovereignty.
The Afghan government took charge of thousands of insurgent prisoners at Bagram military prison on Monday even as it clashed with the United States over the fate of hundreds of inmates.
The handover of the controversial high security prison, sometimes referred to as "the other Guantanamo", had been hailed a victory for Afghan sovereignty as America prepares to withdraw combat troops by the end of 2014.
But the ceremony marking the transition at the prison next to an air base north of Kabul was overshadowed by America's refusal to hand over the last inmates.
US commanders have stopped the transfer of about 30 Taliban prisoners, reportedly over concerns that they will be released by the Afghan government. A spokesperson for US forces would not say who they were, or why they were held.
Six hundred detainees seized since the handover was agreed on March 9 have also yet to be given to Afghan control.
Another 50 prisoners from outside Afghanistan, most from Pakistan, are not covered by the agreement and will also remain under American control.
Disagreement over the fate of the prisoners caused Hamid Karzai, the Afghan president, to issue a terse statement at the weekend warning that any delay in the handover of Bagram "is considered a breach of the Afghan national sovereignty".
There is also dispute over how long American forces can detain suspected insurgents that they capture from now.
Senior US officers stayed away from the ceremony.
Both sides signed a memorandum of understanding about the handover in March, paving the way for the 10-year strategic pact between the two countries signed in April.
Jamie Graybeal, a spokesperson for US forces, said "While some 99% of the detainees captured before March 9 have already been transferred to Afghan authority, we have paused the transfer of the remaining detainees until our concerns are met regarding the intentions of the Afghan government to fulfil the terms of the memorandum."
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