A new report collated from hundreds of testimonies gathered over 10 years said most of those detained are denied access to family or lawyers.
Amnesty said torture has become so institutionalised that many police stations have an informal “officer in charge of torture” or OC Torture.
Amnesty’s Africa director, Netsanet Belay, said the indiscriminate round-ups of hundreds of suspects who were tortured in a “screening” to find Islamic extremists was more like a “medieval witch hunt”.
Nigeria’s government and military have responded to previous Amnesty International reports of abuses with promises to investigate.
Meanwhile, the death toll in a building collapse at a televangelist’s church complex in the country has risen to 80, an official said.
Ibrahim Farinloye, of the Nigerian Emergency Management Agency, announced the toll as search operations continued at TB Joshua’s Synagogue, Church of All Nations, on the outskirts of Lagos, Nigeria’s commercial capital.
South Africa has said 67 South African citizens died in the September 12 collapse of a guesthouse at the church complex.
Officials have not clarified whether the South African fatalities were among the larger group of 80 dead cited by the Nigerian government.
“Search and rescue missions are still continuing after which we will know for sure how many citizens we have lost,” South Africa’s president, Jacob Zuma, said at a meeting of local government officials in Johannesburg.