Security forces also recovered a cache of arms and ammunition in the raid on their camp, the army said.
Gunmen in four speed boats targeted the military checkpoint in southern Bayelsa state on Friday, authorities said.
Piracy and organised crime linked to oil theft are common in the region.
Soldiers destroyed the camp in neighbouring Rivers state and are now trying to track down others who escaped, according to a statement from the Joint Task Force (JTF) in the Niger Delta.
Other items recovered included three speed boats, communication gadgets and generators, it said. –BBC