The early morning blast shook islanders out of bed across metropolitan San Juan and shattered windows across the bay in colonial Old San Juan, one of many neighborhoods where onlookers gaped at the thick smoke boiling north toward the Atlantic Ocean.
The fire was contained by Friday afternoon, according to chief firefighter Pedro Vazquez, but more than a dozen of the plant's 40 fuel tanks were still burning. Firefighters were spraying the rest with cold water and foam to reduce the risk of further blasts.
The cause of the explosion at the Caribbean Petroleum Corp. in the suburb of Bayamon was unknown.
Gov. Luis Fortuno said only one person had required treatment for smoke inhalation, and two others suffered minor injuries at the U.S. Army's Fort Buchanan base, adjacent to the fuel plant that supplies Gulf gas stations across the island.
Several drivers were also hurt when the explosion shattered glass in their cars, but firefighters said all the plant workers were safe.
Marcial Orlando Felix, the top local official for the U.S. Bureau of Alcohol, Tobacco, Firearms and Explosives, said a special team from the mainland would investigate the blast but would have to wait until the fire is out to enter the plant.
The 12:30 a.m. explosion was the equivalent of a 2.8 magnitude earthquake, according to the Puerto Rico Seismic Network. Police and FBI agents were also investigating graffiti that was found Friday after the blast in a highway tunnel in the capital with the message: "Boom, fire, RIP, Gulf."
"Everything is very preliminary at this point but obviously we're looking into the graffiti and it's a concern," Figueroa Sancha said.
The tanks at Caribbean Petroleum hold about 10 percent of the gasoline consumed in the U.S. Caribbean territory, according to Consumer Affairs Secretary Luis Rivera Marin. He said there was no risk of shortages, but the government ordered gas prices frozen anyway after some service stations raised prices amid rumors to the contrary.
The flames, which could be seen from miles away, intensified in the hours following the explosion and police chief Jose Figueroa Sancha said it would likely take several days to put out the fire.
The U.S. Federal Aviation Administration diverted plane traffic because of the smoke.
Authorities evacuated 125 families from the poor neighborhoods near the plant because of concern about contamination from the smoke. At a nearby top-security prison, armed guards stood watch as the first of the 2,500 inmates were loaded onto buses for prisons elsewhere on the island.
Experts from the Environmental Protection Agency were traveling to Puerto Rico to help monitor the capital's air quality. In the meantime, environmental authorities urged residents near the plant to keep their windows shut.
Associated Press writers Laura N. Perez Sanchez and Manuel Ernesto Rivera contributed to this report.