BAGRAM: Afghanistan said Monday it had taken control of a controversial prison set up by US troops, but is yet to iron out disagreements over the fate of hundreds of inmates.

A move hailed by Kabul as a victory for sovereignty, analysts say it is largely symbolic as Nato prepares to leave Afghanistan after more than a decade fighting the Taliban, leaving Afghan security personnel in charge in late 2014.

Major questions remain over the immediate and long-term fate of more than 3,100 inmates, which include Taliban fighters and terror suspects, held at Bagram, sometimes referred to as the Guantanamo Bay of Afghanistan.

Around 50 foreigners are not covered by the agreement, and hundreds of other Afghans arrested since the transfer deal was signed on March 9 are also being held at the Parwan Detention Facility, outside the Bagram US airbase north of Kabul.

Afghan officials on Monday presided over a small handover ceremony, which was marked by a low attendance among US and Nato officers. “I’m happy that today we are witnessing a glorious ceremony that marks the handing over of responsibilities of Afghan prisoners to Afghans themselves,”acting defence minister Enayatullah Nazari told the ceremony.

Afghan military police commander Safiullah Safi said that 3,182 prisoners had been formally handed over to Afghan military police, following a six-month transition.

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.

Karzai's spokesman, Aimal Faizi, says there are disagreements over the interpretation of the deal and that more than 600 people detained since March 9 have not yet been transferred to Afghan custody.He told AFP that talks on Saturday between Karzai and the US ambassador, and the US commander in Afghanistan had been “tough” and said the 600 yet to be transferred were being held illegally in contradiction of the MoU.

Jamie Graybeal, a Nato spokesman, says 99 per cent of detainees held before March 9 are under Afghan authority and that the transfer of the rest has been put on hold, pending concerns about the intentions of the government to fulfil the terms of the MoU.

Graybeal said the United States 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.

In March, Afghanistan's human rights commission detailed torture in prisons run by the Afghanistan's intelligence service and police force. Speaking to AFP, the NDS intelligence service spokesman Shafiqullah Taheri rejected the claims, saying that rights activists regularly visit detention centres.

In January, Afghan investigators said inmates at Bagram had been tortured, although a report made public gave few details of the allegations made by prisoners.

Interestingly former inmates and relatives of detainees currently at the prison have expressed concern that conditions may worsen. A former mujahideen commander, who was arrested in 2003 and held at Bagram and Guantanamo Bay in Cuba, said the Americans treat their prisoners better than the Afghans.

Ghaleb, 55, declined to give his second time but described himself as an influential elder in his hometown in eastern province Nangarhar. “I have heard the same from many other prisoners who were tortured by government people.

I have seen many prisoners who say they were much happier to have been kept in jails under the command of Americans,” he told AFP. Abdul Waheed Wafa, analyst and director of the Afghanistan Centre at Kabul University has said the move is largely symbolic and believes the Americans will still detain some high profile suspects at Bagram or at other locations.