The report on Thursday cited "systematic practice of torture and ill-treatment of suspects held" at the Temara centre, as well as a "series of breaches of Moroccan law and international human-rights standards".
"Detainees have been blindfolded and handcuffed during interrogation. Some have been stripped or suspended from the ceiling in contorted positions. Many reported being beaten or threatened with the arrest and rape of their wife or female relatives," Amnesty said.
The London-based organisation added: "The detainees have been systematically denied their right to legal counsel from the beginning of the judicial process. Those detained have been held in secret, sometimes for months, and have been denied access to their families or to the outside world."
"Morocco's failure to take action on persistent allegations of torture and ill-treatment in the Temara and other detention centres undermines the country's recent progress in the field of human rights," it said.
Some 2000 people have been arrested, charged with "terrorist activities", since the bombings in the commercial capital, Casablanca, in May 2003.