The US on Monday formally handed control to Afghanistan of more than 3,000 detainees at the controversial Bagram prison, but disagreements remain over the fate of hundreds of inmates.

Kabul has hailed the transfer of what has in the past been dubbed the Guantanamo Bay of Afghanistan as a victory for sovereignty as NATO prepares to hand over full national security to Afghans and withdraw its combat troops by the end of 2014.

Analysts, however, say the move is more symbolic than substantial and human rights advocates have raised concerns about abuses of administrative detention.

Questions remain over the fate of the inmates, who include Taliban fighters and terror suspects, 50 foreigners not covered by the agreement, and hundreds of Afghans arrested since the transfer deal was signed on March 9.

Afghan officials on Monday organized and presided over a small handover ceremony at the prison, officially called the Parwan Detention Facility but more commonly referred to Bagram after the neighboring US airbase north of Kabul.

There was only a paltry attendance among US officers as the Afghan flag was erected over the prison, marking the transfer.

"We transfer more than 3,000 Afghan detainees into your custody," said Colonel Robert Taradash, the highest ranking US official at the ceremony.

"I'm happy that today we are witnessing a glorious ceremony that marks the handing over of responsibilities of Afghan prisoners to Afghans themselves," Afghan acting defense minister Enayatullah Nazari said at the ceremony.

Sixteen inmates, dressed in new shalwar khameez, were freed as part of the ceremony. Three of them who spoke to AFP all insisted they had been held on baseless accusations.

Afghan President Hamid Karzai demanded authority over the prison as conditional to addressing long-term Afghan-US relations and possible legal immunity for US troops, the key to troops remaining in the country after 2014.

But the Memorandum of Understanding (MoU) governing the handover is not legally binding and more than 600 people detained since March 9 have not yet been transferred.

Afghan army chief of staff, General Sher Mohammad Karimi, said he expected that a "small misunderstanding" between the Afghans and the Americans would be resolved.

Jamie Graybeal, a NATO spokesman, said the US retained the authority to capture and detain suspects, but intended to continue to transfer Afghan detainees to Afghans. Foreign detainees will remain under US control and American advisers will also stay at the prison until March 9, 2013, he added.

Afghan officials dispute NATO's right to hold detainees, saying that anyone arrested in extenuating circumstances has to be handed over within 72 hours.

Advocacy group the Open Society Foundations last week raised concerns about holes in the March agreement, the risk of indefinite detention and voiced fears that Afghan detention without judicial review could be subject to abuse.

AFP