At least 38 have died, he said, and 134 survived. Seventeen people remain unaccounted for, he said.
The Philippine coast guard is leading the search, with divers from the Red Cross and the military involved.
Three Americans are among the survivors. They are Rhome and Chip Nuttall and Larry Drake, according to Gordon.
The MB Nirvana had just departed Ormoc City in Leyte province bound for the town of Pilar on Camotes Island, east of Cebu Island, about noon local time Thursday when the disaster occurred.
The boat, which is 27 meters (89 feet) long, was barely 200 meters (more than 650 feet) from the shore when it capsized, Philippine coast guard Lt. Christopher Ganet said.
He said those who have been rescued are being taken to hospitals in the area around Ormoc.
High winds, seas hamper efforts
Video footage from the scene showed people of all ages, including a small child, being brought ashore in small inflatable craft. Some survivors were laid on the concrete waterfront, while others were wheeled away on stretchers.
Rescue workers were battling to find those unaccounted for before it gets dark.
Lt. James Reyes, a Philippine navy spokesman, said navy divers were helping in the search and rescue efforts.
They have underwater flashlights and other equipment to enable night diving, he said, and will try to carry out dives if the water conditions allow.
Gordon said Red Cross staff was on the pier in Ormoc with blankets and meals to assist those who made it back to shore.
Officials are trying to get divers to the scene, he said, and had hoped to put a helicopter in the air but have been prevented by “zero visibility” in poor weather conditions.
“The winds are really bad, and the seas are really bad,” he said.
Investigators will examine what caused the boat to capsize.
A CNN Philippines reporter quoted the coast guard as saying the boat had left port too quickly and people stood up, throwing the boat off balance. Gordon said he understood the boat overturned because of high winds.
It’s monsoon season in the Philippines, which adds to the likelihood of poor weather.
Gordon: Passengers were ‘poor folks, simple folks’
Gwendolyn Pang, secretary-general of the Philippine Red Cross in Manila, described the vessel as a commercial “pump boat” or banka, which is essentially a canoe-style craft with outriggers powered by a small engine. They’re widely used across the Philippines for transporting people and goods as well as for fishing.
Gordon said the boat would operate three times a day on the route from Ormoc to Camotes Island.
“The passengers would have been farmers or fishermen, or ordinary businessmen — common folks,” he said.
“They are not very well off, otherwise they would be on better vessels or take the plane. But obviously, these are poor folks, simple folks who are trying to eke out an existence.”
This style of outrigger boat has no cabins, he said, which should make it easier for divers to find anyone trapped under the canopy or keel of the vessel.
Gordon said Red Cross staff at the scene was checking who was on board and how many were children. Officials have also brought body bags in case they are needed, he said.
Many may not even be able to afford a proper burial, he added.
Hospitals take in survivors, bodies
Dr. Rolando Tomaro, medical director of Ormoc Doctors’ Hospital, told CNN that four hospitals in the Ormoc area were receiving people caught up in the disaster.
At the Ormoc Doctors’ Hospital, 21 survivors and 16 bodies had been brought in, he said. The dead included an 8-month-old child and his 13-year-old brother, he said.
Ten survivors remain in the hospital under observation, he said, but none are in a critical condition.
“We have to monitor them for signs of respiratory distress because of the near-drowning incident,” he said. “They would have ingested seawater, so we are monitoring them. As of now, they are all stable.”
Tomaro, who has been a surgeon at the hospital for 20 years, said it was the first time anything like this had occurred.