The 25 suspects were found dead in their cell one day after being arrested in December, Communications Minister Issa Tchiroma Bakary said in a press conference yesterday.
They were part of a group of 56 detainees, and the cause of their deaths is still being determined, he said.
"I can already state here that at this stage of investigation, no evidence has been established to corroborate that these persons were deliberately killed," Bakary said.
In January, the Network of Human Rights Defenders in Central Africa, based in the capital, Yaounde, cited "reliable sources" in claiming that 50 Boko Haram suspects had suffocated to death in their cells before being buried in a mass grave.
The group's report accused the army of engaging in rights violations including torture "with impunity."
Boko Haram has been fighting a nearly 6-year insurgency against the Nigerian government, killing thousands and carrying out mass kidnappings, including of schoolgirls.
Cameroon's northern region was repeatedly targeted by Boko Haram before the country signed up to participate in a multinational force that has dislodged the group from a score of northeastern Nigerian towns in recent weeks.
Nigeria acknowledged on Thursday that it is getting help from regional security operatives amid reports that South Africa and other foreign contractors are involved in the fight against Boko Haram.
Also on Thursday, Islamic State militants in the Middle East accepted a pledge of allegiance from Boko Haram, though it is unclear how the groups might be able to cooperate effectively.
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