The tremor struck early on Saturday, rattling the city of Ponce, and damaging some buildings. There are no immediate reports of casualties.
The epicentre was in the sea off the southern coast, but no tsunami advisory has been issued.
A number of aftershocks were also recorded in the 90 minutes following the initial event according to the US Geological Survey.
Also shaken were the towns of Guánica and Guayanilla, where hundreds of homes were damaged or destroyed in January's 6.4 magnitude earthquake, which killed one person.
The quake comes as Puerto Rico nears the two month mark of its lockdown to prevent the spread of the coronavirus.
Governor Wanda Vázquez tweeted that rescue crews were fanning out across the area and that she would shortly be travelling there to meet with those affected in person.
“If your infrastructure is damaged, you must leave with your face mask on and your emergency backpack,” she said, urging people to remain calm.
The mayor of Ponce, María Meléndez, posted pictures of the damage to her city and asked people to "avoid going to the city centre until we make sure everyone is safe."
Víctor Huérfano, director of Puerto Rico’s Seismic Network, told the Associated Press that while it’s understandable many people are afraid and surprised by the most recent earthquake, it’s not unusual given the seismic activity that began in the region in late December.
“In the long run, it’s decreasing, but you can have peaks,” he said, adding that he expects strong aftershocks to continue.
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