Nato forces in Afghanistan have stopped sending prisoners to some Afghan jails after reports of torture and have asked Kabul to investigate allegations of abuse by members of a US-backed paramilitary police force.

The ban on transfers revives concerns about human rights in Afghan prisons, first raised in 2011 by a United Nations report. The report detailed widespread abuse, including the ripping out of detainees' toenails and the twisting of their genitals, and prompted Nato-led troops to halt prisoner transfers for several months.

Handovers resumed after inspections and training but a new report by the same UN office is expected to confirm there are still serious problems, a few months after torture concerns prompted Britain's defence minister to drop plans to transfer prisoners to Afghan jails.

The report's broad findings were detailed in an official email released last year by the Ministry of Defence as part of a court case challenging the UK moratorium on handovers. The report has been repeatedly delayed since last summer, when it was originally expected to be released.

"The report would conclude that torture was continuing to take place at NDS [National Directorate of Security] and ANP [Afghan national police] facilities across Afghanistan, whilst recognising that there had been a decline in the prevalence of abuse at some facilities," said the email, which detailed a meeting between UK embassy diplomats and UN officials working on the report.

It highlighted a counter-terrorism jail run by the intelligence services in Kabul as one major problem, "with a large number of serious recent allegations surfacing", and named a man who subsequently became head of the Afghan spy service, Asadullah Khaled, as a "principle [sic] culprit" for the torture of Taliban prisoners.

The Nato-led International Security Assistance Force (Isaf) confirmed a ban on transfers to some jails, but did not confirm if it was a reaction to the UN report.

"Based on concerns over detainee treatment at certain Afghan detention facilities, Isaf suspended the transfer of detainees to these facilities," spokesman James Graybeal said in a written response to questions. He declined to say which prisons or areas of the country had problematic treatment of prisoners, so it was not clear if they were the same jails identified in the 2011 report.

Then, nearly half of prisoners interviewed by Afghanistan's intelligence agency said they had been tortured, while a third of those arrested by Afghan police reported abuse, although the report said the ill-treatment was not "institutional or government policy".

Nato has also raised torture concerns about a controversial US-backed programme to bolster security forces through militia-like groupings of men armed and paid to defend their home villages or districts, known as the Afghan Local Police (ALP).

"Isaf has formally requested that the GIRoA (Government of the Islamic Republic of Afghanistan) ministry of interior investigate instances where torture by the ALP has been alleged," Graybeal said. The Afghan government "has committed to uphold its human right obligations", and was co-operating with efforts to end torture, he added.

But Afghan officials said the claims of mistreatment were unfounded, and there had been no official notice that handovers had been halted by the US or Nato.

"We reject this, we have received no evidence from the Americans that there is torture in our jails," said National Directorate of Security spokesman Shafiqullah Tahiri. "The human rights commission and defence commissions visit the prisons and interview prisoners. They are not being tortured."

• Additional reporting by Mokhtar Amiri