The report, released earlier this week, says most of the ill treatment occurred in facilities run by the police or intelligence service, The New York Times reported Friday.
Afghan officials took exception to statements in the report, endorsed by the International Security Assistance Force, which said the abuse was "systematic."
Aimal Faizi, the spokesman for President Hamid Karzai, said ISAF makes weekly visits to prisons run by the Interior Ministry and the national security agency.
"If there's a problem, why aren't they saying it when they visit?" he asked.
The report contains a statement by ISAF commander Gen. John R. Allen that he and his deputy had written to the Afghan government about 80 cases of abuse.
Allen had already stopped transferring detainees to the facilities because international law prohibits the transfer of any detainee to a government where there are "substantial grounds for believing that he would be in danger of being subjected to torture."
Some 635 detainees in facilities around Afghanistan were interviewed for the report.