The shallow quake hit just before 6:30 am (2230 GMT) about 20 kilometres (12 miles) from the village of Barcelona on the east of Mindanao island, USGS said.
Many people were sleeping when the strong shaking jolted them from their beds.
The local seismological agency said no damage was expected from the earthquake.
In Lingig municipality, where Barcelona is located, local disaster officer Ian Onsing said he was woken by the tremor.
"The shaking was quite strong. The things around here were moving. I guess, the shaking took around 10-15 seconds," he told AFP by telephone.
"So far, there are no reported casualties or damage. We are now monitoring the shores for any rough movement."
In the municipality of Hinatuan, about 25 kilometres north of Barcelona, local disaster officer Jerome Ramirez saw appliances "moving for around 30 seconds" from the strong shaking.
He also said there had been no reports of injuries or damage in coastal communities in the area.
"Now we are just monitoring for possible aftershocks," Ramirez told AFP by telephone.
A series of aftershocks were felt in some areas in Mindanao, with the strongest at 6.3 magnitude about 36 kilometres east of Barcelona, according to USGS.
"Aftershocks are happening here every two minutes, but we're glad it's not as strong as the earthquake this morning," Onsing said.
Earthquakes regularly strike the Philippines, which sits along the Pacific Ring of Fire, an arc of intense seismic and volcanic activity that stretches from Japan through Southeast Asia and across the Pacific basin.
Most are too weak to be felt by humans but strong and destructive quakes come at random with no technology available to predict when and where they will happen.
In December, a 7.6-magnitude quake struck off Mindanao, briefly triggering a tsunami warning.
That sent residents along the east coast of the island fleeing buildings, evacuating a hospital and seeking higher ground. At least three people died.
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