The body of a helicopter pilot has been found in waters off Port Hedland in Western Australia after his chopper came down on Wednesday.

The Pilbara Ports Authority says the 44-year-old's body and the wreckage of the craft were found on Saturday and a recovery operation is being planned.

The chopper came down about 30km off Port Hedland with a second pilot, believed to be aged 64, rescued from a life raft shortly after the crash.

The aircraft was carrying no passengers at the time and crashed as it approached the China-bound bulk carrier MV Squireship to pick up a marine pilot.

"Our thoughts are with the man's family and loved ones, to whom we send our sincerest condolences," the ports authority said in a statement.

The Australian Transport Safety Bureau will investigate the crash while WA police will prepare a report for the coroner.