About 1000 suspected Boko Haram militants died in detention in the first half of 2013 alone, London-based rights organization, Amnesty International, said Tuesday.
Some of the dead were beaten and shot without getting medical attention while others die due to harsh detention conditions such as over-crowded jails and starvation.
"The evidence we've gathered suggests that hundreds of people died in military custody in 2013 alone. This is a staggeringly high figure that requires urgent action by the Nigerian government," Lucy Freeman, Amnesty International's deputy Africa director, said in a statement.
"The details of what happens behind locked doors in these shadowy detention facilities must be exposed, and those responsible for any human rights violations brought to book."
The Nigerian army said it has not seen the report and will respond when it is made available to them.
A large proportion of these deaths are reported to have happened in Giwa military barracks, Maiduguri in Borno State, and Sector Alpha, commonly referred to as 'Guantanamo' and Presidential Lodge (known as 'Guardroom') in Damaturu, Yobe State."
Detainees in these detention centres told Amnesty International that people die daily in "both Giwa and Sector Alpha from suffocation or other injuries due to overcrowding, and starvation. Some suffered serious injuries due to severe beating and eventually died in detention due to lack of medical attention and treatment."
Some of the atrocities perpetuated in these camps are summary execution and detainees being shot in the legs during interrogations.
"Hundreds have been killed in detention either by shooting them or by suffocation... There are times when people are brought out on a daily basis and killed. About five people, on average, are killed nearly on a daily basis," a senior army officer told h asked not to be named told Amnesty International.
"International standards, as well as Nigerian laws, require that deaths in custody must be investigated thoroughly and impartially," said Ms Freeman. "Detainees have human rights and these must be respected in all instances."
Hundreds of suspected Boko Haram militants are held in mostly secret detention centres across the country without charge and no access to lawyers and family members.