The incident happened on Friday at the Caribbean Petroleum Corp (CPC) facility.
Reports say at least two people were hurt and that 350 people had to be evacuated.
Reuters said the fire destroyed 11 of the oil facility’s 40 storage tanks, which contained products including bunker fuel, jet fuel and gasoline.
Governor Luis Fortuno ordered the closure of all schools in the San Juan metropolitan area, while the U.S. Coast Guard shut down San Juan Bay.
“It’s impossible to say what happened right now. We are focused on containing the fire and ensuring everyone’s safety,” Fortuno said.
The CPC facility included a 48,000 barrel-per-day (b/d) refinery, but this was not in operation, according to the CPC website.
Reuters said fire and smoke could be seen for miles.