Most of the torture is happening at a base that has also been used by US and French troops, the international rights organisation said in a new report on Thursday.
Amnesty's report documented 101 cases of arbitrary arrest and torture by Cameroonian troops between 2013 and 2017 at more than 20 different sites.
Some of the victims were tortured to death, it said.
Though Boko Haram originated in Nigeria, the group - which is affiliated with the Islamic State of Iraq and the Levant (ISIL, also known as ISIS) - has carried out frequent attacks in Cameroon, Chad and Niger.
Boko Haram attacks have killed more than 20,000 people and displaced 2.7 million in the region, according to aid agency figures.
"We have repeatedly and unequivocally condemned the atrocities and war crimes committed by Boko Haram in Cameroon," said Alioune Tine, Amnesty International's regional director for West and Central Africa.
"But, nothing could justify the callous and widespread practice of torture committed by the security forces against ordinary Cameroonians."
Tine condemned the "horrific violations" by the Cameroon forces which amount to "war crimes".
Of the 101 documented individuals, 32 claimed to have witnessed the death of a fellow prisoner, according to the NGO.
Victims included women, the disabled and the mentally ill, the report said.
"They asked me to tell them if I knew members of Boko Haram," Amnesty cited a prisoner as saying. "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,"
"They beat me half to death," he added.
A Cameroon defence ministry spokesman accused Amnesty International of "bad faith" and of trying "to transform killers into victims".
"Our army is professional and disciplined," Cameroon's army spokesman Colonel Didier Badjeck told Reuters news agency. "It has better things to do than to spend time justifying itself against people who have preconceived ideas."
US, France 'should investigate'
Amnesty said most of the torture was carried out at two intelligence services sites - Rapid Intervention Battalion (BIR) headquarters in Salak and the General Directorate of External Research (DGRE) facility in Yaounde.
The group said US and French military personnel were present at the BIR base in Salak
It urged the two governments to investigate whether their military personnel knew that torture was taking place on the site, and whether or not their assistance "has contributed to the commission of these crimes and violations".
The US Africa Command said it had not received any reports of human rights abuses by Cameroonian forces at the base mentioned.
"To date, US Africa Command has not received any reports of human rights abuses by Cameroonian forces at either of these locations," Robyn Mack, a spokeswoman for the US military’s Africa Command, said in a statement.
"Any foreign military unit that receives security assistance receives training on the law of armed conflict and human rights law."
French Defence Ministry officials did not immediately comment.