The remains will be transported to a port in Coron, Palawan, coast guard spokeswoman Commodore Noemie Cayabyab said in a statement.
AFP watched hours earlier as disaster agency workers carried coffins to a cemetery in the resort town, intended for the temporary burial of victims of the fire that tore through the M/V June Aster on Wednesday.
The first 30 bodies arrived by sea earlier on Saturday as forensic specialists began the painstaking process of identifying the remains.
The confirmed death toll now stands at 76, including five bodies recovered in the immediate wake of the incident.
The ship sits grounded about 7.5 kilometres off the coast.
One-metre deep graves have been dug to hold the victims’ remains until DNA testing is completed, Kristine Ablana, a tourism official serving as an official spokesperson, told reporters on Saturday.
Relatives will be brought to identify personal items that may have belonged to family members.
“Once someone is able to verify… that this photo or these belongings are indeed those of their relative, they will be asked to provide a DNA sample,” Ablana said.
Thirty passengers, including two Chilean nationals, and 13 crew have been rescued, according to the coast guard.
Around a dozen people are believed to remain unaccounted for.
Cayabyab said in a radio interview that the fire had begun in the cargo hold, then tore through the ship within seconds.
“From the time that they heard the loud explosion, the appearance of smoke, and then fire. It spread very quickly,” she said of survivors’ accounts.
“Everything happened in seconds,” she said, adding that those who made it off the ship had not even had time to put on life jackets.
Near the pier where the bodies were to be returned, an emotional Josenit Mayo, 40, told AFP her daughter had been aboard the ferry, returning from the capital Manila for a family visit.
Hundreds of people desperate for news about the incident have taken to leaving comments on the Facebook page of a local mayor, searching for relatives, friends and even a dog.
The archipelago nation of 116 million has a long history of disasters involving inter-island ferries that ply its seas.
In January, a triple-decker ferry carrying more than 340 people sank off the southern Philippines, killing at least 52 people.
On Thursday, the company that owns the M/V June Aster, Atienza Interisland Ferries Inc, said it was fully cooperating with the investigation. (AFP)
