The 7.2-magnitude quake struck off the coast of the island of Mindanao in the Philippines at 8.23pm (GMT) on Friday.
The quake was measured at a depth of 10km, 68km south of the city of General Santos, the Tsunami Centre added.
The hazardous tsunami waves are possible off the coasts of the Philippines and Indonesia, it said.
The warning urged residents of threatened coastal areas to "stay alert for information" and follow instruction from authorities.
The US Geological Survey measured the quake at 6.8.