"The new authorities in Libya must stamp out arbitrary detention and widespread abuse of detainees," the Amnesty report "Detention Abuses Staining the New Libya" released on Thursday said.
Libya's National Transitional Council has been Libya's de facto ruler since rebels overthrew Muammar Gaddafi last month.
The London-based group said it uncovered a pattern of "beatings and ill-treatment of captured Gaddafi soldiers, suspected loyalists and alleged mercenaries in western Libya. In some cases there is clear evidence of torture in order to extract confessions or as a punishment.''
"There is a real risk that without firm and immediate action, some patterns of the past might be repeated. Arbitrary arrest and torture were a hallmark of Colonel Gaddafi's rule," said Hassiba Hadj Sahraoui, Amnesty International's Deputy Director for the Middle East and North Africa.
Since late August, armed militia have arrested and detained as many as 2,500 people in Tripoli and al-Zawiya, Amnesty said.