The U.S. Geological Survey put the magnitude of Tuesday's quake at 6.4, while the local seismology agency said it was 6.5. The quake was centered near San Julian town in Eastern Samar province and prompted residents to dash out of houses and office workers to scamper to safety.
There were no immediate reports of injuries or major damage from the new quake.
Let our news meet your inbox. The news and stories that matters, delivered weekday mornings.
Meanwhile, rescuers worked overnight to recover bodies in the rubble of a supermarket that crashed down in Monday's quake, which damaged other buildings and an airport in the northern Philippines.
The bodies of five victims were pulled from Chuzon Supermarket while seven other people died in hard-hit Porac town in Pampanga province, north of Manila, said Ricardo Jalad, who heads the government's disaster-response agency.
An Associated Press photographer saw seven people, including at least one dead, being pulled out by rescuers from the pile of concrete, twisted metal and wood overnight. Red Cross volunteers, army troops, police and villagers used four cranes, crow bars and sniffer dogs to look for the missing, some of whom were still yelling for help Monday night.
Authorities inserted a large orange tube into the rubble to blow in oxygen in the hope of helping people still pinned there to breathe. On Tuesday morning, rescuers pulled out a man alive, sparking cheers and applause.
"We're all very happy, many clapped their hands in relief because we're still finding survivors after several hours," Porac Councilor Maynard Lapid said by phone from the scene.
Philippine seismologists said the back-to-back quakes in the last two days were unrelated and caused by different local faults.
One of the world's most disaster-prone countries, the Philippines has frequent earthquakes and volcanic eruptions because it lies on the so-called Pacific "Ring of Fire," a seismically active arc of volcanos and fault lines in the Pacific Basin. A magnitude 7.7 quake killed nearly 2,000 people in the northern Philippines in 1990.