Some of the victims were tortured to death, the rights group said.
Though Boko Haram originated in Nigeria, the Islamic State-affiliated group has carried out frequent attacks in Cameroon, Chad and Niger in its bid to create an Islamic caliphate around Lake Chad. Boko Haram attacks have killed more than 20,000 people and displaced 2.7 million in the region, according to aid agency figures.
Amnesty International said it had found 101 people who said they were held in secret and tortured by the Rapid Intervention Battalion (BIR) and the General Directorate of External Research (DGRE), Cameroon's intelligence services, between March 2013 and March 2017.
"They asked me to tell them if I knew members of Boko Haram. That's when the guard tied my hands and feet behind my back and started to beat me with an electric cable, while throwing water on me at the same time," Amnesty cited a prisoner as saying. "They beat me half to death," he added.
Of the 101 documented individuals, 32 claimed to have witnessed the death of a fellow prisoner, according to the Amnesty report "Cameroon's Secret Torture Chambers: Human Rights Violations and War Crimes in the Fight Against Boko Haram".
The group said most of the torture was carried out in two sites: the BIR headquarters in Salak and a DGRE facility in Yaounde.
Amnesty said US and French military personnel were present at the BIR base in Salak and called on the two governments to investigate whether they were aware that illegal detention and torture was taking place on site.
Amnesty said its delegates had observed French troops at the base in May 2015. It also said it had still and video images “clearly showing the regular presence of US personnel in numerous locations across the base, including making use of a makeshift gym and a trailer converted into an office.
Atrocities such as the kidnapping of more than 200 schoolgirls from the Nigerian village of Chibok in 2014 persuaded Western countries, especially the US and France, to provide counter-insurgency assistance to some of the countries affected, including intelligence and training.
The US Africa Command said it had not received any reports of human rights abuses by Cameroonian forces at the base mentioned.
French Defence Ministry officials did not immediately comment.
(FRANCE 24 with AFP, REUTERS)