When a propeller of a ship rotates it increases the velocity of water near it.The velocity of fluid in the front of the ship is relatively less.so as per bernoullis principle the pressure at the back must decrease so the ship must feel a suction and move back but why does it move in forward direction?

There is indeed drag caused by the "suction" effect behind the boat. You can see that in the swirls and eddy's in the wake directly behind the boat. But the forward force from the propeller as it accelerates water backwards is greater than the drag, so the boat moves forward.