A cargo of several tons of toxic chemical fertiliser that was on board the ship and had prevented recovery work from progressing was recently removed.
Officials say the remains of the dead will be brought to the city of Cebu for processing and DNA identification.
Most of the bodies recovered so far have detached limbs or heads and disintegrating flesh after months in the water, forensic scientists working for the recovery effort have said.
|Divers have said it will take up to two weeks to search the entire ship [EPA]
Dr Renato Bautista, chief of the Philippines' National Bureau of Investigation’s Disaster Victims Identification unit said the DNA matching would be carried out in the laboratory of the International Commission for Missing Persons in Sarajevo in Bosnia.
Samples in batches of 100 will be sent and results are expected within two or three weeks, he told the Philippine Daily Inquirer newspaper.
The Princess of the Stars was on an overnight journey from Manila to Cebu when it sank in heavy seas caused by Typhoon Fengshen.
Only 56 people are known to have survived the disaster, one of the worst in maritime disasters in a country where millions rely on ferries to travel between the Philippines' hundreds of islands.
Around 350 bodies were recovered in the days after the disaster, but the rest are believed to be still inside the ship.
In 1987 more than 4,000 people died when the Dona Paz ferry collided with an oil tanker and sank.
A report by the government's Board of Marine Inquiry, which conducted an investigation into the Princess of the Stars sinking, blamed the ship's captain and owners, Sulpicio Lines, for the disaster.
According to the report the captain miscalculated the risks when he left Manila despite storm warnings.
It also said Sulpicio Lines should be held liable because it did not stop the boat from leaving the Manila port.