The US Geological Survey said the earthquake measured magnitude 6.1 and struck at a depth of 38 kilometres.
Government seismologist Jane Punongbayan said it was centered under the ocean 205 kilometres northwest of Zamboanga city and was too deep and far from urban areas to cause any damage or injuries. She said aftershocks were expected.
Zamboanga city police director Angelito Casimiro said people attending Mass at a Roman Catholic shrine exchanged glances when the ground began to shake mildly, but the ceremony proceeded after the shaking stopped.
The Philippine archipelago lies in the Pacific "Ring of Fire," where earthquakes and volcanic activities are common.
A magnitude-7.7 quake killed nearly 2,000 people on the northern island of Luzon in 1990.

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