Amnesty International said in a report that the suspects, including women and children, were beaten, water-boarded and forced into stress positions.
The cases allegedly happened between 2013 and 2017, and dozens of detainees died as a result, it added.
Cameroon's government has not commented. Boko Haram frequently carries out attacks in the country.
The Islamist group, based in neighbouring Nigeria, has killed more than 1,500 civilians in Cameroon since 2014, and abducted many others, Amnesty said.
Victims described a least 24 methods of torture at more than 20 different sites, the report said.
In one of those places, it said, there was the presence of US and French military personnel. There was no evidence that foreign forces were involved, but Amnesty urged both countries to investigate the allegations.
The report added that people suspected of supporting the militants were often being detained without evidence.
Who are Boko Haram?
Suspected Boko Haram fighters have been "brutally tortured" by security forces in Cameroon, a rights group says.