The detainees reported 16 torture methods, including beatings, suspension from walls or ceilings, electric shocks and near-asphyxiation.
Some detainees said their genitals were twisted with a wrench-like device while others reported being kept in extremely hot or cold conditions and being denied food and water.
The report by the UN Assistance Mission in Afghanistan (UNAMA) said the number of detainees saying they had been ill-treated or tortured in the past two years -- 278 of 790 interviewed in nearly 130 facilities -- was 14 per cent lower than the previous period.
A detainee who was held in an intelligence facility said he was kicked and punched on his first day of detention and beaten with a water pipe the following day. On the third day, he said, they used a device to "squeeze my sexual parts till I cried," at which point he confessed to being a Taliban insurgent, the report said.
"I was scared because they threatened they would destroy my sexual organs. I just said anything and they wrote it down and I put my thumb prints on the papers. I thought I might die if they destroyed my sexual organs," he was quoted as saying.
"There is no systematic torture, and if some cases have been reported, those are the acts of individuals who have misused their authority, and we are fully committed to investigate and arrest those individuals," he said.
But the report said torture investigations were flawed and alleged perpetrators were rarely prosecuted, fired or disciplined.
"Afghanistan's efforts to prevent torture and ill-treatment have shown some progress over the last two years," said UNAMA head Nicholas Haysom. "More remains to be done, however, and I welcome the new administration's immediate attention to end these practices.
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