Pentagon officials have described the former machine shop at Bagram air base, 65km north of Kabul, as a screening centre, The Times said.
"Bagram was never meant to be a long-term facility, and now it's a long-term facility without the money or resources," an unnamed Pentagon official, who knows the facility and compared it to the one at Guantanamo, was quoted as saying.
"Anyone who has been to Bagram would tell you it's worse" than the Guantanamo prison, the official said.
The Guantanamo jail has triggered a worldwide debate about the treatment of prisoners, many of whom were held for years without trial before a June 2004 Supreme Court ruling.
The Times said some of prisoners had been held at Bagram for two or three years and had no access to lawyers or to hear the allegations against them.
Administration officials have compared the legal limbo at Guantanamo to Bagram's, according to The Times, which said that the military had kept Bagram secret for a longer period, by barring photographs and by refusing to make prisoners' names public.
The International Committee of the Red Cross is allowed to visit, The Times said.
Former prisoners, military officials and soldiers have described facilities where men are held in wire cages, sleep on foam mats on the floor and, until a year ago, used buckets as latrines, The Times said.
Top Pentagon officials refused to be interviewed about the base, The Times said.
A spokesman, James Yonts, said the military in Afghanistan was "committed to treating detainees humanely and providing the best possible living conditions and medical care in accordance with the principles of the Geneva Convention", The Times said.