The body count is only reflective of this year, the human rights group said. In some instances, prisoners are suffocated or die as a result of gunshot wounds or other injuries suffered during interrogations because prisoners have no access to medical care. In other instances the deaths come as a result of starvation, Amnesty International said.
The group issued a statement Tuesday calling on the Nigerian government to investigate the camps as a matter of urgency.
"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," said Lucy Freeman, Amnesty International's deputy Africa director.
Boko Haram is a militant Islamist group that's suspected of carrying out numerous terrorist attacks and waging a guerrilla campaign against the Nigerian government.
Regardless of prisoners' crimes, they still must be treated humanely, Freeman said.
"International standards, as well as Nigerian laws, require that deaths in custody must be investigated thoroughly and impartially," she said. "Detainees have human rights and these must be respected in all instances."