San Juan, Puerto Rico (CNN) -- Investigators don't know if the massive fire at a fuel storage facility near San Juan was deliberately started or was an accident, the agent in charge of the FBI's San Juan office said Monday.

The blaze, which started with an explosion at the Caribbean Petroleum Corp. facility in Bayamon municipality early Friday, was extinguished Sunday, firefighters said. Some of the tanks continued to smolder and crews stood ready to fight any flare-up.

"We don't know if it's a crime scene," said FBI Special Agent Luis Fraticelli. "We don't know if it's an accident, so we're not making any determinations at this point until our experts do their work, do their analysis and then provide input to us as to what they feel happened here."

Puerto Rico is a territory of the United States.

The FBI is investigating graffiti found on two San Juan tunnels that referred to a fire, Special Agent Harry Rodriguez said Friday. A spray-painted message on the tunnels, less than three miles apart, said: "Boom, fire, RIP, Gulf, Soul, ACNF." Caribbean Petroleum owns the Gulf Oil brand, but Rodriguez said he did not know what ACNF referred to.

Hundreds of firefighters battled the blaze, which began with an explosion early Friday morning. That explosion shook the ground with the force of a 2.8-magnitude earthquake, authorities said. Flames shot into the air while plumes of thick, black smoke hovered over the region.

Agents from the FBI and the U.S. Bureau of Alcohol, Tobacco, Firearms and Explosives were investigating to determine whether the explosion was an act of sabotage or an accident.

Seventeen tanks were destroyed by flames and the initial explosion.

Puerto Rico's governor, Luis Fortuno, said the main priority of his government is to counter any long-term effects of air and water pollution caused by the disaster. Representatives from the Environmental Protection Agency have been checking air quality near the fire.

"We're not finding levels that would be of concern," said Bonnie Bellow, EPA spokeswoman. She said the fire had been so intense because it was "burning off chemicals that are part of the fuel."

About 600 displaced people stayed in shelters on Sunday night, but many were being sent home. Dr. Lorenzo Gonzalez, Puerto Rico's health secretary, tests conducted on the air and water showed no reason for concern.

Because they were placed in close proximity in the facilities, everyone in the shelters and all the emergency personnel were vaccinated against the H1N1 flu virus as a precaution, Gonzalez said.

President Obama declared an emergency in Puerto Rico, which frees up federal aid.

Fortuno said the blaze has cost the island at least $6.4 million.

The governor sought to allay fears over gasoline supplies. Caribbean Petroleum owns 200 gas stations in the island and several inland distribution facilities, and supplies much of the island's fuel.

Puerto Rico will receive 3.6 million gallons of regular gasoline, more than 1 million gallons of premium gasoline and more than 1 million gallons of diesel fuel to help make up for what may have been lost, Fortuno said.

The company has been cited for violations of the federal Resource Conservation and Recovery Act, the main law in the United States that deals with the disposal of solid and hazardous wastes, according to EPA spokeswoman Bellow. Caribbean Petroleum is under a corrective-action plan, she said.

CNN's Rafael Romo and Arthur Brice contributed to this report.