This was the strongest quake in a series of three earthquakes of magnitude 5.0 to 5.9 to hit Batangas in the Luzon province, about 55 miles (90km) south of Manila, around 3pm local time or 7am GMT.
The USGS said the quakes occurred over a period of about 20 minutes.
Hundreds of people fled to higher grounds fearing a tsunami, authorities have said.
Lito Castro, head of the provincial disaster council, told local radio: "Residents in the coastal villages in two towns have evacuated to safer ground after the earthquakes. The people were afraid the earthquakes would generate a tsunami."
But the head of the Philippine Institute of Volcanology and Seismology, Renato Solidum, said the earthquakes had not been powerful enough to cause a tsunami.
A Reuters reporter said feeling a tremor for over a minute in the Makati business district of Manila.
AFP reporters said they saw people running out of office buildings in Manila's financial district.
Batangas officials said there were no reports of casualties but some areas were affected by power cuts and cracks have been reported in homes and some commercial buildings.
Landslides have also been reported in some towns and a portion of a Catholic church tower reportedly collapsed.
Local television network ABS CBN broadcast images of passengers rushed to leave the Batangas International Port, which is near the epicentre of the earthquakes.
The strongest quake is reported to be at a depth of 27 miles (43km).
The region had experienced temors since earlier this week.
Reuters
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