The 6.1 magnitude quake struck northwest of the capital on Monday, the USGS said, heavily damaging an airport and sending terrified locals fleeing swaying high-rises.
The worst of the damage was in the province of Pampanga, which was the site of most of the 11 fatalities, disaster officials said.
More than 100 others were injured by falling rubble, including in Manila, according to police.
The toll could rise as crews fanned out across the mostly rural region to assess damage in isolated hamlets that lost power and communications in one of the area's strongest tremors in years.
"They can be heard crying in pain," she said of those trapped. "It won't be easy to rescue them."
More than 400 aftershocks have been registered since the initial quake, Philippine seismologists said.
Scores of rescuers in the town of Porac were using cranes and jackhammers to peel back the pancaked concrete structure of a four-storey market building where the Red Cross said 24 people were unaccounted for.
"Every minute, every second is critical in this rescue," Cris Palcis, a volunteer sniffer dog handler, told AFP.
"Time is short for the people under the rubble so we have to be quick."
Pampanga Governor Lilia Pineda told journalists that rescuers could still hear at least one person trapped beneath the rubble, but the digging was proceeding delicately to avoid accidentally crushing the survivor.
The quake also damaged several centuries-old churches which were crowded with worshippers in recent days as the majority-Catholic Philippines marked the Easter holiday.
Father Roland Moraleja, who is based in Porac, said the 18th century belfry of Saint Catherine of Alexandria church collapsed in the quake.
"It was the only part left from the old church," he told AFP. "The historical value is now gone, but we are hopeful that it will rise again."
High-rise buildings in the capital swayed after the tremor struck on Monday evening, leaving some with large cracks in their walls.
Thousands of travellers were stranded after aviation authorities shut down the secondary Clark Airport, which is located on the site of the former US military installation that lies about an hour's drive north of the capital.
It was still closed on Tuesday as officials assessed the heavy damage to the terminal building and some cracking on the air traffic control tower.
The quake was centred on the town of Castillejos, about 100 kilometres (62 miles) northwest of Manila, local geologists said.
Seismologists put the main tremor at 6.3 initially, but subsequently downgraded it to a 6.1 magnitude.
Dani Justo, a martial arts instructor, told AFP she was at her southern Manila home when the quake struck.
"The clothes hanging on our line were really swaying. My shih tzu (dog) dropped flat on the ground," she added.
The Philippines is part of the Pacific "Ring of Fire", an arc of intense seismic activity that stretches from quake-prone Japan through Southeast Asia and across the Pacific basin.