The 5.9-magnitude quake struck the southern city of Surigao and surrounding areas, causing some walls to collapse, government seismologists and civil defence officers said.
One woman died of a heart attack while at least 29 people were injured, local television reports added.
The new earthquake was just one of over a hundred aftershocks to hit Surigao City on Mindanao island since a 6.5-magnitude quake on February 10 left eight dead and over 250 injured, mainly due to falling objects.
The Philippines lies on the so-called Ring of Fire, a vast Pacific Ocean region where many of the world's earthquakes and volcanic eruptions occur.
Before the February 10 quake, the last lethal one to hit the country was a 7.1-magnitude tremor that left over 220 people dead and destroyed historic churches when it struck the central islands in October 2013.
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