The biggest of the quakes, with a magnitude of 7.4, hit about 20 kilometres (12 miles) off Manay town in the Mindanao region just before 10 am (0100 GMT), according to the United States Geological Survey.
An aftershock with a magnitude of 6.7 rocked the same area almost 10 hours later, one of scores that followed the morning quake.
Both came 11 days after a magnitude 6.9 earthquake killed 75 people and injured more than 1,200 in Cebu province in the central Philippines, according to official data.
Three miners tunnelling for gold were killed when a shaft collapsed in the mountains west of Manay during the larger quake, rescue official Kent Simeon of Pantukan town told AFP.
One miner was pulled out alive and several others were injured in the remote hamlet of Gumayan, he said.
"Some tunnels collapsed, but the miners managed to get out," Simeon said.
One person was killed in Mati city when a wall collapsed, while two others suffered fatal heart attacks, city disaster official Charlemagne Bagasol told AFP.
Another person was crushed by falling debris in Davao city, more than 100 kilometres west of the epicentre, police said.
A third heart attack victim died in the town of Montevista, provincial disaster official Ednar Dayanghirang told reporters.
Philippine authorities issued tsunami warnings shortly after the morning quake as well as for the early evening one, ordering evacuations along the eastern seaboard, though no big waves had been monitored.
The Pacific Tsunami Warning Center lifted its own alert for the Philippines, Palau and Indonesia at around noon.
- 'People screamed and ran' -
Wes Caasi, an official in Tagum city, northwest of Manay, told AFP that a government event at the city hall descended into chaos as panicked attendees fled. "They screamed and ran."
Caasi said she saw city workers scrambling down a metal Christmas tree they were decorating outside the bulding when the first quake struck.
Nice Eugenio from Tagum city told AFP the strong aftershock knocked out power in her neighbourhood.
"It lasted only a few seconds, but (it) was very strong. I felt like I was going to faint from nervousness," she said.
A plane that had just landed in Davao city was shaken by the aftershock, which prevented passengers from disembarking immediately, an AFP photographer on board said.
AFP journalists later saw Davao residents queueing for fuel at crowded petrol stations at night.
Witnesses and officials said the quakes appeared to have caused only minor damage, while the Philippine seismology office said it had recorded more than 300 aftershocks.
There were no reports of collapsed buildings but "there were landslides and our bridges exhibited cracks", Davao Oriental provincial governor Nelson Dayanghirang told the ABS-CBN network.
"Some buildings were damaged," he said.
More than 200 patients were evacuated from the Manay district hospital, where tents were set up outside to shelter them after the building's foundations cracked, Dayanghirang said.
Classes were suspended and non-essential workers were sent home, the provincial government said on Facebook.
- 'Shaking was so strong' -
Christine Sierte, a teacher in Compostela town, said violent shaking started when she was in an online meeting, and the ceilings of some buildings later fell though no one was injured.
"It was very slow at first, then it got stronger... That's the longest time of my life. We weren't able to walk out of the building immediately because the shaking was so strong," she told AFP.
Earthquakes are a near-daily occurrence in the Philippines, which is situated on the Pacific "Ring of Fire", an arc of intense seismic activity stretching from Japan through Southeast Asia and across the Pacific basin.
An 8.0-magnitude quake off Mindanao island's southwest coast in 1976 unleashed a tsunami that left 8,000 people dead or missing, the Philippines' deadliest natural disaster.
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