Police in the Philippines have filed multiple murder charges against the owner and crew of a ferry that capsized shortly after pulling out of port, leaving more than 50 dead.

Rio Tan of Ormoc City police said the charges were filed with the local prosecutor as the 36-ton MB Kim Nirvana was lifted from the water.

Regional coastguard commander Pedro Tinampay said at least 59 people died, while 145 survived, including all 18 crew members.

Capt Tinampay said a marine investigation has begun and it will determine how many people were aboard the vessel.

The ship flipped over off Ormoc City when it was lashed by strong waves after leaving the port en route to one of the Camotes Islands, about 20 miles south.

Capt Tinampay said earlier that the movement of cargo inside the hold might have contributed to the accident. The ferry was carrying heavy construction materials and bags of rice.

Ormoc, a regional economic and transportation hub of about 200,000 people, is in a disaster-prone eastern region that is regularly hit tropical storms and typhoons that blow in from the Pacific.