The Afghan government has rejected allegations of torture in its prisons, calling them politically motivated.
The allegations, which appear in an as-yet unpublished UN report, suggest that in some prisons detainees have been beaten and given electric shocks.
They prompted Nato to suspend prisoner transfers to some facilities.
But Kabul said the report aimed to disrupt the handover of control of security back to Afghans as foreign troops prepare to leave by 2014.
The criticism came from Afghanistan's interior ministry and intelligence agency, the NDS - neither of which have seen the UN report, which is reportedly set for publication within days.
But they co-operated in its production, allowing UN investigators free access to prisons across the country, says the BBC's Quentin Sommerville in Kabul.
They said they strongly rejected the allegations in the report - which have been disclosed to the BBC and include prisoners being beaten with rubber hoses, threatened with sexual assault and in some cases given electric shocks, our correspondent says.
"We consider these [allegations] unfounded excuses for not transferring the prisoners and prisons to the Afghans, and it will damage the process," Interior Minister Bismillah Mohammadi told a news conference in Kabul, referring to the transition of security to Afghan agencies.
Rahmatullah Nabil - head of the NDS, which runs the majority of the jails where mistreatment has been reported - also rejected the report.
He said he had received more than 600 reports from the United Nations and human rights groups that had visited Afghan prisons in recent months, none of which reported problems.
"When they visit the prisons and write reports, but then give a different report to the media, it raises questions," he told the joint news conference.
Prisoner transfers in Kandahar province had already been halted in July, but another eight facilities were added to that list following the report's revelations - in Herat, Khost, Lagman, Kapisa and Takhar, as well as the NDS' Counter-Terrorism prison, known as Department 124.
The Nato-led International Security and Assistance Force (Isaf) has also suspended the transfer of detainees to two prisons run by the Afghan Police in Kunduz and Tarin Kowt.