The 6.5 magnitude quake hit the island of Mindanao, the US Geological Survey said, causing locals to run to safety in the same area where a strong tremor killed eight people on Tuesday.
The powerful shaking caused serious damage to a condominium building in the major southern city of Davao, about 45 kilometres (28 miles) from the epicentre.
Nine people were hurt at the building, and rescuers believed at least one was trapped in the rubble, a local disaster official said.
Five people were killed in nearby Cotabato province, including a local official who was crushed to death, a police officer said.
A hotel partially collapsed in another area, but a disaster official said the building had already been evacuated.
Locals have been left terrified by a string of powerful quakes, and hundreds of aftershocks since the first powerful tremor struck on October 16.
“I panicked and I rushed outside. I was afraid the building might collapse,” said Beth Lancian, a restaurant cashier in Davao. “There’s been an earthquake almost every week.”
President Rodrigo Duterte was in his hometown of Davao when the shaking began, but his spokesman said he was unharmed.
Some 12,000 people were already in shelters on Mindanao island before Thursday’s quake hit, the government said, either because their homes have been destroyed or they were too afraid to return to their residences.
The Philippines suffers regular tremors as part of the Pacific “Ring of Fire”, an arc of intense seismic activity that stretches from Japan through Southeast Asia and across the Pacific basin.
In the 6.6 magnitude quake on Tuesday, a teenage boy was crushed by a falling wall as he tried to escape his school in Magsaysay, the town spokesman told AFP.
Rock and landslides unleashed by the violent shaking killed four others, while a collapsing wall crushed a man, authorities said.
Nearly 400 people were hurt, including some seven pupils and teachers hurt escaping their crumbling elementary school.
The area was still suffering the effects of a 6.4-magnitude quake that hit less than two weeks ago, killing at least five people and damaging dozens of buildings.
Residents fled homes across the Mindanao region and a mall caught fire in the city of General Santos shortly after the quake struck on October 16.
Hundreds of people were still displaced two weeks after that quake when the second one struck earlier this week, forcing thousands more from their homes.
One of the deadliest quakes to hit the Philippines recently was in April, when 16 people were killed as a building near the capital Manila collapsed and the secondary Clark airport was shut down after damage to the passenger terminal.
High-rise structures in the capital swayed after the April quake, leaving some with large cracks in their walls.
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