Joseph BetiAssomo made the confession recently in Yaounde, days after a suspected Ambazonian separatist was tortured beyond repair by the armed forces.
Images circulating on social media featured a man being kicked, beaten, and rolled in mud by men in uniform.
While some sources believed the suspected separatist, popularly known as General, did not survive the torture, the minister stayed silent on the topic.
Mr Assomo revealed that the soldiers will be held accountable, as investigations are being carried out.
Cameroon has denied previous claims of the use of excessive force on Anglophone separatists and civilians. Several rights groups have criticised Mr Biya's approach to the unrest in Southern Cameroons.
Scores of civilians are believed to have been shot and killed, beaten to death, tortured to death in detention, and a lot more. Allegations that the Biya regime has all rubbished.