The charges were filed late on Friday in the central city of Ormoc over the sinking of the Kim Nirvana ship, according to regional police head Chief Superintendent Asher Dolina.
An initial police investigation and interviews with survivors showed the vessel abruptly turned in waters off the central port of Ormoc on Thursday, causing it to capsize, Dolina told AFP.
"They were not careful, showing there was an intent to kill. They were
A total of nineteen people
Under Philippine law, murder is punishable by up to 40 years imprisonment.
The police investigation is separate from a coast guard inquiry, which will primarily determine the cause of the mishap.
However, the coast guard may also recommend criminal and administrative charges.
"We filed the charges as soon as we could because we don't want the suspects to leave the country," Dolina said.
Fifty-six people were confirmed dead from the sinking, Ormoc city councillor Godiardo
Overloading of cargo and passengers might have been to blame for the disaster, according to Ebcas, who helped oversee rescue operations.
Survivors reported seeing up to 150 sacks of cement and more of rice and
Bloated bodies spilled out of the Kim Nirvana's wooden hull as a crane lifted it from the water and placed it on Ormoc port, Ebcas added.
Poorly-maintained boat
The city councillor said the death toll stood at 56 with 142 survivors. His toll was higher than the 45 reported by the coast guard, which was based on the ship's passenger list, though the guard counted the same number of survivors.
The coast guard earlier said the 33-tonne ship could carry 194
"The ship might not be too overloaded in terms of passengers, but imagine the weight of its cargo," Ebcas said.
Each sack of rice, cement and
Passengers on the ferry's regular route from Ormoc to the Camotes islands regularly bring supplies from the city to their remote fishing villages.
Search operations with rescue divers were stopped on Friday before the ship was lifted
Poorly-maintained, loosely-regulated ferries form the backbone of maritime travel in the Philippines, a sprawling archipelago of 100 million people.
Many sea disasters occur during the typhoon season, which starts in June.
Frequent accidents in recent decades have claimed thousands of lives, including the world's worst peacetime maritime disaster in 1987 when the Dona Paz ferry collided with an oil tanker, leaving more than 4,300 dead.