The prison at the Bagram air base houses senior al-Qaeda suspects
A US military review is to recommend an overhaul of the entire Afghan prison and judicial systems, Pentagon officials have confirmed.
Concerns about recruitment by the Taliban within local prisons are among the issues being addressed in a major review of US detention policy.
Reform of the US-run Bagram air base is said to be a key plank of the review, which has not yet been released.
Last month the BBC uncovered widespread allegations of abuse at the facility.
The BBC spoke to 27 ex-inmates around the country over two months, most of whom alleged they had been beaten, deprived of sleep and threatened with dogs at Bagram.
In 2002, two Afghan detainees died after being repeatedly struck by American personnel.
Prisoners at the controversial facility are currently refusing privileges available to them, as part of a protest about their basic rights.
Bagram is the main prison for people detained by US forces in Afghanistan. Most detainees there have been arrested on suspicion of militancy - the US considers them "unlawful combatants" who can be detained indefinitely.
Pentagon officials confirmed the existence of the review, which is being conducted against the background of allegations of abuse at Bagram.
Among the issues being considered, US officials are concerned at how Afghan authorities treat detainees and are seeking to build up a viable judicial network in Afghanistan.
The review was conducted by US marine commander Maj Gen Douglas M Stone, the New York Times reported on Monday. He is widely credited with transforming American detention practices in Iraq.
Gen Stone's key recommendation is for militants to be separated from more moderate detainees who are being held on charges unrelated to militancy, the newspaper said.
Under the proposals, the US could help fund and construct an Afghan-run prison to hold extremists.
The review also reportedly recommends that the remaining prisoners should be taught vocational skills and classes in moderate Islam, to help re-integrate them into society.
It also makes the case for more training for new Afghan prison guards, prosecutors and judges.
The findings form part of a 60-day review of the ongoing war being undertaken by the new US commander in Afghanistan, Gen Stanley McChrystal.
Details about the new policy first emerged when the Wall Street Journal reported aspects of the review last month, but two officials who have read or been briefed about the report gave further details about its contents to the New York Times and the BBC.
Lack of lawyers
The BBC's correspondent in Kabul, Martin Patience, says there are serious issues concerning infrastructure and overcrowding in prisons.
According to figures from the Afghan justice ministry, there are 34 prisons and an estimated 15,000 prisoners in the country. It is unknown how many inmates are connected to the Taleban.
Our correspondent says the Afghan government has rented at least 12 other buildings to accommodate prisoners.
He added that another big concern is prisoners having no access to lawyers or a fair judicial system. As of May, there were about 500 lawyers in the country - that is one lawyer for every 60,000 Afghans.
Main base for US-led forces
Prison on the site has capacity for 1,000 prisoners
About 600 Afghans and foreign al-Qaeda suspects held there
US calls inmates "unlawful combatants"
Inmates have no right to challenge detention in US courts
In May President Obama said he would not release more photographs showing abuse by US military officials of prisoners in Iraq and Afghanistan.
He said that every case of abuse had been dealt with and warned that releasing the images could further inflame opinion against the US, potentially endangering US troops serving abroad.
But President Obama has also said that the US is examining an alleged massacre of hundreds of prisoners who had surrendered to a US-backed warlord in Afghanistan in 2001.
Amid allegations that the Bush administration resisted efforts to investigate, he told officials to "collect the facts" surrounding the incident.
Reports of the alleged massacre first surfaced in 2002 but there has been no formal investigation.
Afghanistan is a renewed priority with the US administration, with concerns running high about the resurgence of the Taliban, correspondents say.
In a recent trip to Afghanistan US military chief Adm Mike Mullen highlighted the urgency for more troops in the country.
The New York Times also reported that he had issued a confidential message to military service chiefs emphasising the need to ensure prisoners were treated properly.
US and UK forces are currently engaged in a major operation to combat Taliban militants in the south of the country.