Ill-treatment and lack of respect for due process have long helped foster mistrust in the government and fuelled the 10-year Taliban insurgency, with torture a crime under Afghan and international law, according to a report published on Monday.
The UN mission in Afghanistan said it had "compelling evidence" that Afghan intelligence officials at five centres "systematically tortured detainees for the purpose of obtaining confessions and information."
There were credible allegations of torture at two other National Directorate of Security (NDS) centres, it said.
The United Nations noted the use of torture was not NDS or government policy, and welcomed being given full access to detainees.
In an annex to the report, the intelligence service said: "Torture methods such as electric shock, threat of rape, twisting of sexual organs, etc, are methods that are absolutely non-existent in the NDS."
The findings were based on interviews with 379 pre-trial detainees and convicted prisoners at 47 detention centres across the country, conducted from October 2010 to August 2011, said the UN.
It said 46 per cent of the 273 detainees interviewed who had been held by the NDS "experienced interrogation techniques ... that constituted torture".
Detainees described being hung by the wrists from the wall or ceiling; and being beaten especially with rubber hoses, electric cables or wires or wooden sticks and most frequently on the soles of the feet, the report said.
Electric shock, stress positions including forced standing, removal of toenails and threatened sexual abuse were among other forms of torture that detainees reported.
Routine blindfolding and hooding, and denial of access to medical care in some facilities were also reported. The United Nations documented one death in Afghan custody from torture in Kandahar in April.
More than a third of 117 detainees interviewed after being held by police for alleged insurgent activity "experienced treatment that amounted to torture or to other cruel, inhuman or degrading treatment", it said.
Significantly, the United Nations said the US-led international military were involved in the capture and transfer to Afghan custody of some detainees.
The UN mission called on Afghanistan to take every step to end and prevent torture, and provide accountability for all acts of torture.
The interior ministry, which controls the police, and the NDS on Monday told AFP they were studying the report and would react in the coming days.
The US-led NATO mission in Afghanistan said it has stopped transferring detainees to certain centres owing to evidence of torture.
