Amnesty said Britain, Canada, Denmark, the Netherlands and Norway had signed "memorandums of understanding" and other accords on prisoner transfers with the Afghan authorities, and that Belgium, France, Germany and Sweden could do as well.
The agreements, it said, "do not fulfil the absolute and non-derogable legal obligation not to put anyone in a situation where they are at risk of torture or other ill-treatment".
Isaf, which comprises some 40,000 troops from 37 nations, is trying to stabilise the government of Hamad Karzai, which has been battling the Taliban for control of the country since US-led forces ousted the group from the power in 2001.
James Appathurai, a Nato spokesman, said the military alliance had no evidence that any prisoners were being abused and did not plan to build its own jails just in case.
"Nato has no proof of ill-treatment or of torture of detainees that its forces have transferred to the Afghans," he said.
In its report, Amnesty urged Isaf to "immediately declare a moratorium on any further transfers of detainees to the Afghan authorities and take responsibility for the custody of such detainees until effective safeguards against torture and other ill-treatment are introduced in the Afghan detention system".
It called on them not to rely on memorandums of understanding as a guarantee that prisoners would not be tortured once they are handed over, and help train prison staff and reform the prison system.
It also urged Afghanistan to reform the NDS and allow independent monitors into all detention facilities.
President Hamid Karzai's senior spokesman, Homayun Hamidzada, said: "The laws of Afghanistan do not allow torturing of prisoners. If they're tortured, we take this issue very seriously."
He said the administration was reviewing the watchdog's report.
Appathurai said: "It's true there are concerns. This is precisely why the allies have invested, and a lot, in the reform of the Afghan institutions, including the NDS. It's the only appropriate and acceptable way to improve the situation."
But "Afghanistan is a sovereign country", he said. "It's not up to Nato to put a parallel detention system in place on Afghan territory."