The charges were filed late yesterday 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 reckless on purpose," Dolina said.
Under Philippine law, murder is punishable by up to 40 years imprisonment.
Also Read
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 Ebcas told AFP.
Survivors reported seeing up to 150 sacks of cement and more of rice and fertiliser in the ship's cargo area before it capsized in relatively calm seas, he said.
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.
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 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 fertiliser weighs 50 kilos (110 pounds), and 150 sacks would easily add 7,500 kilos to the ship's load, excluding passengers, he said.