The United Nations says torture in Afghan prisons continues to be widespread despite its recommendations in a similar report in 2011.
More than half of the 635 detainees interviewed by UN investigators said they had been ill-treated or tortured.
The Afghan government says the claims are exaggerated, the BBC's Quentin Sommerville in Kabul says.
Nato's force in Afghanistan, Isaf, has suspended the transfer of detainees to facilities named in the report.
The report, by the United Nations Assistance Mission in Afghanistan (Unama), focused on detainees in facilities run by both national and local police forces and the intelligence services, the NDS, between October 2011 and October 2012.
It identified 14 methods of torture and ill-treatment practices, including beatings, a threat of execution and sexual abuse. Some were given electric shocks to extract confessions or obtain information.
The number of incidents in police custody had risen from 35% to 43% compared with the previous 12 month period; although NDS facilities had seen a fall from 46% to 34% over the same period.
Unama said that, although the government had implemented some recommendations in its 2011 report, from training to inspections and directives, there appeared to be little follow up in the pursuit of offenders.
"Unama found a persistent lack of accountability for perpetrators of torture with few investigations and no prosecutions for those responsible," said Georgette Gagnon, Unama's Director of Human Rights.
"Without deterrents and disincentives to use torture, including a robust, independent, investigation process, criminal prosecutions and courts' consistent refusal to accept confessions gained through torture, Afghan officials have no incentive to stop torture."
Afghan President Hamid Karzai has insisted that prisoner custody is a matter of Afghan sovereignty and has demanded the US hand over any Afghans it is holding, our correspondent says.
But Isaf commanders have warned that given the current high levels of abuse, that cannot possibly take place any time soon, he adds.