KABUL - Almost a third of all detainees recently transferred to Afghan control have been tortured and Afghanistan's spy agency is operating secret facilities to avoid international scrutiny, a United Nations report released on Sunday said.

The findings could complicate the already thorny issue of how to manage the security transition ahead of the withdrawal of NATO-led troops from Afghanistan by the end of next year. Hundreds of detainees are being transferred from NATO to Afghan control as part of that transition.

Based on interviews with hundreds of detainees between October 2011 and October 2012, the 139-page report found "credible and reliable evidence" that more than half of those interviewed experienced torture or abuse.

Of the 79 detainees interviewed who were transferred from NATO to Afghan control during the 12 months, 25 were tortured, a rise of seven per cent over the previous year's report.

"The (Afghan) government's efforts to address torture and those of ISAF (NATO's International Security Assistance Force), although significant, have not resulted in a marked improvement and reduction in the use of torture," said the report.

"This raises concerns at a time when the government is taking over almost full responsibility for conflict-related detainees from international military forces."

The European Union said in a statement it was "deeply concerned" by the report and urged the Afghan government to "bring the perpetrators of such acts to justice".

A spokesman for the National Directorate of Security (NDS) referred Reuters to President Hamid Karzai's office for comment. Karzai's spokesman said a statement would be released on Monday.

The U.N. Assistance Mission in Afghanistan (UNAMA) interviewed 635 conflict-related detainees held at 89 facilities across Afghanistan by Afghan security forces and the NDS.

The report is the second by UNAMA to highlight widespread abuse within the Afghan detention system.

The United States and other ISAF nations halted transfers to nine Afghan-run facilities after the mission's October 2011 report alleged that hundreds of detainees -- including children -- held by NDS and the Afghan security forces were tortured or abused.

"This situation raises continuing concerns about states' legal obligations prohibiting them from transferring detainees to another state's custody where a substantial risk of torture exists," Sunday's report said.

NATO-led forces in Afghanistan have been handing over detainees to Afghan control gradually ahead of the withdrawal of most international forces.

The report outlines a harrowing list of fourteen methods of torture, including beatings with pipes and wooden sticks, twisting of genitals, extracting fingernails, electric shocks and threats of execution and rape.

The report also includes a statement by an unnamed NDS official in Kabul who confirmed the agency's use of torture and secret facilities for detainees.

"NDS has several secret places in which they detain and torture people," the official said.

The official said NDS intentionally moved tortured prisoners to their headquarters in Kabul to evade outside scrutiny.

"All tortured detainees were taken out of their cells that are located in one building and they were transferred to another building inside the same compound to hide them."