The U.S. Geological Survey said the 8:54 a.m. (1254 GMT) quake hit 8 miles (13 kilometers) southeast of Guanica at a shallow depth of 3 miles (5 kilometers).
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Another 4.6 magnitude earthquake was detected near the island about an hour later, according to the National Weather Service.
Puerto Rico's Electric Power Authority said outages were reported across much of southern Puerto Rico and crews were assessing possible damage at power plants.
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Bárbara Cruz, a prosecutor who was in the southern coastal city of Ponce when the new quake hit, said concrete debris hit the sidewalk as buildings continued to crumble.
"Everyone is out on the street," she said.
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RELATED: Hundreds homeless after 6.4 quake strikes Puerto Rico
There were no immediate reports of injuries.
The quake, which initially had been calculated at magnitude 6.0, was the strongest shake yet since a magnitude 6.4 quake - the strongest to hit the island in a century - struck before dawn on Tuesday, knocking out power across Puerto Rico and leaving many without water.
More than 2,000 people remain in shelters, many fearful of returning to their homes, and others unable to because of extensive damage.
Hundreds of quakes have shaken the island since the new year, though most were too slight to be felt.
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NASA reported Friday that the quakes had moved the land in parts of southern Puerto Rico as much as 5.5 inches, based on satellite images before and after the temblors.
Víctor Huérfano, director of Puerto Rico's Seismic Network, told The Associated Press that he expects still more aftershocks as a result of the latest large one.
"It's going to re-energize an unstable situation," he said, adding that seismologists are studying which faults were activated. "It's a complex zone."
Hundreds of thousands of Puerto Ricans are still without power and water, and thousands are staying in shelters and sleeping on sidewalks since Tuesday's earthquake. That temblor killed one person, injured nine others and damaged or destroyed hundreds of homes and several schools and businesses in the island's southwest region.