Yan Pieter Yarangga, a resident from the town of Biak, said hundreds of people ran out of their homes and fled beaches with some racing for higher ground for fear of a tsunami.
"I ran too, I was afraid there would be a second quake,'' he said.
Wednesday's quake that hit Papua's coast was located more than 3,000km from the country's capital, Jakarta.
Indonesia straddles a series of fault lines that make the vast island nation prone to volcanic and seismic activity.
A giant quake off the country on December 26, 2004, triggered the Indian Ocean tsunami that killed 230,000 people, half of them in Indonesia's westernmost province of Aceh.