The fire destroyed 11 of the Bayamon oil facility's 40 storage tanks, which contained products such as jet fuel, bunker fuel and petrol.
Agents from the US Federal Bureau of Investigations said that they would help local authorities in their investigation into what caused the blast.
Carlos Garcia, the president of the Government Development Bank, said that the explosion was being treated as an accident.
Petrol station queues
Housewife Tamara Rivera, 37, said the force of the explosion rattled her bedroom door and set off car alarms throughout her Puerto Nuevo neighbourhood.
"At first I thought it was an earthquake, but when I went outside, I saw the big orange glow. It looked like daylight over there," she said.
The US Coast Guard set up a safety zone in the part of San Juan Bay closest to the scene of the fire, and no vessels were allowed to enter the zone without permission from the port captain.
The Caribbean Petroleum Corp (CPC) facility also included a 48,000 barrel-per-day (bpd) refinery, but this was not in operation, according to the CPC website.
There were no immediate details on the extent of damage.
CPC has more than 200 service stations in Puerto Rico to market Gulf brand petrol and diesel.
Queues formed at petrol stations as residents feared a shortage, but Fortuno said the island had a week's supply.
Luis Rivera Marin, Puerto Rico’s consumer affairs secretary, was meeting Puerto Rico's suppliers and retailers to consider whether to impose a price freeze.
Agency officials are monitoring petrol stations to see if prices have been put up, he said.