The third time you encounter Master Kohga, he creates a raft to attack you.

Master Kohga: Raft

At the East Mine, Kohga makes a large motorized raft with two footsoldiers on it. Go to the small raft at the end of the dock and hop on. Check on the controls to start moving. When you are close enough to hit Kohga, be sure to press the button to let go of the controls before you try to attack.

This time, when you stun Kohga and he disappears, his raft stays there, so feel free to use it. It is not as fast or maneuverable, but it also won't roll side to side.

Later versions of his raft will put a force field around him, but he will turn off the force field sometimes to throw a large bomb at you. That gives you a chance to shoot at him.