He said ferry operator Sulpicio Lines as well as maritime experts had been summoned to the inquiry which aims to determine whether the ship was seaworthy and why it was allowed to leave port during Typhoon Fengshen.
He added that details gathered in the inquiry could be used for a criminal prosecution.
Al Jazeera's Marga Ortigas said the inquiry was expected to conclude its findings within 20 days.
More than 100 divers continued to comb the wreckage of the 24,000-tonne Princess of the Stars in waters off the central island of Sibuyan on Wednesday, but Lieutenant-Colonel Edgard Arevalo, a navy spokesman, said "there are no signs of life".
|Relatives want to know why the ferry was allowed to sail amid a typhoon [AFP]
Rescuers said anyone who had managed to find air pockets in the ship would have suffocated by now.
Divers from the Philippine navy and coast guard cut their way through the ship's hull three days after it capsized in the typhoon on Saturday but found only bodies.
Many more corpses remain inside the ship.
The navy said rescuers were prevented from reaching the ship sooner by roiling seas and lingering strong winds.
Lieutenant Commander Inocencio Rosario, a coast guard diver, said he was hoping for a miracle.
"I hope somebody there is alive," he said. "We have only probed about 15 per cent of the ship."
Only 57 people survived, according to civil defence figures, out of more than 850 people on board.
|Arroyo has vowed to hold the ferry company accountable [AFP]
US divers have joined the ill-equipped Philippine coastguard's recovery effort for bloated bodies of men, women and children who were on the 22-hour trip from Manila to central Cebu when the typhoon struck.
The US has also offered to send an aircraft carrier to help Philippine relief efforts for victims of Typhoon Fengshen that hit the country's south and central regions last weekend.
George Bush, the US president, made the offer during talks with his Philippine counterpart, Gloria Arroyo, at the White House on Tuesday.
Ferry owners summoned
Arroyo said Sulpicio Lines, the owners of the ferry, should be held accountable for one of the country's worst maritime disasters.
"We are holding the ferry company accountable to ensure that we find how this tragedy could have occurred so we can take steps to make sure it never happens again," the Philippine's Daily Inquirer quoted her as saying in Washington on Tuesday.
Angry relatives have asked why the Princess of the Stars was allowed to sail with a typhoon approaching.
Sulpicio Lines, the ship's owner, said it sailed with coast guard approval.
On land, Typhoon Fengshen killed 227 people and left 275 missing in the worst-hit region, with dozens reported killed elsewhere by floods and landslides.
The powerful storm flooded numerous communities and caused an estimated $74.2m in crop damage.
It is now on its way to Taiwan and southwest China.