Seismology agency Phivolcs warned of aftershocks from Friday's magnitude 7.4 quake, which struck in the morning in waters off Manay town in Davao Oriental in the Mindanao region.
At least one person was killed, civil defence official Raffy Alejandro said on Facebook.
The Pacific Tsunami Warning Center issued an update about noon, local time, saying the tsunami threat in the Philippines had passed, having earlier said waves one to three metres high were possible, although warnings from other agencies remained in place.
There were no other reports of casualties from disaster offices in the region contacted by Reuters, but one official in Manay said there were initial reports of damage to homes, buildings and bridges.
The quake was among the strongest in recent years to hit the Philippines, which sits on the Pacific "Ring of Fire" and experiences more than 800 quakes each year.
The US Tsunami Warning System issued a tsunami threat immediately after the quake, saying hazardous waves were possible for coasts within 300km of the earthquake's epicentre.
The earthquake came two weeks after the Philippines experienced its deadliest quake in more than a decade, with 74 people killed on the island of Cebu.
That was a magnitude of 6.9 and also struck offshore.
Philippine President Ferdinand Marcos Jr said authorities were assessing the situation on the ground, and said search-and-rescue teams would be deployed when it was safe to do so.
"We are working round the clock to ensure that help reaches everyone who needs it," Marcos said in a statement.
Phivolcs revised down the magnitude from an initial reading of 7.6 to 7.4, and put the depth of the quake at 23km.
A tsunami warning was issued in Indonesia for its northern Sulawesi and Papua regions, and the PTWC said some coasts in Indonesia and the Pacific island nation of Palau could see waves of up to 1m.
A video of the quake from the Philippine city of Davao posted on social media and verified by Reuters showed office workers holding on to desks, with the creaking noises of structures.
Another showed toppled cabinets and evacuated workers gathering outside.
With AP
