The boat “capsized on Sunday between the city of Limbe and Bakassi. There were dozens of troops on board, including a colonel,” the source told AFP, speaking on condition of anonymity.
The Rapid Intervention Brigade is in the front line of Cameroon’s fight against Boko Haram jihadists in the far north.
“The army has begun searches,” the source said, while another source close to the Cameroon army said at least one body had been recovered.
As well as the troops the boat was also transporting equipment for construction work at a military base on the Bakassi peninsula, where the Brigade has helped to bring security after a previous spate of hostage-takings.
Though Boko Haram originated in Nigeria, the Islamic State-affiliated group has carried out frequent attacks in Cameroon, Chad and Niger.
Cameroon’s Far North region, which borders Nigeria, has seen a resurgence in attacks blamed on Boko Haram after months of relative calm.
Last week two bombers blew themselves up in northeastern Cameroon killing 15 people in an attack blamed on Boko Haram.
Some 200,000 Cameroonians from the Far North region have fled their villages in fear of the violence.