The fire at Chevron's refinery in Richmond, about 10 miles northeast of San Francisco, was out early Tuesday morning, San Francisco Bay area-based KGO-TV reported.
Chevron spokeswoman Heather Kulp, however, said at a 5 a.m. news conference that officials were conducting a controlled burn.
Smoke and flames from the fire, which began around 6:15 p.m. Monday, could be seen for miles.
It was contained and a shelter-in-place order lifted on Monday night.
Doctors Medical Center in San Pablo, a town near the Chevron refinery in Richmond, said about 200 people had sought help and more patients were arriving. Kaiser's Richmond Medical Center also said several dozen people came to the emergency room complaining of shortness of breath, but none was seriously ill.
Residents said they heard loud blasts around the time the fire broke out, although Chevron officials could not confirm those reports.
Daniela Rodriguez told the Contra Costa Times that she heard a "big boom." The 23-year-old resident said about an hour passed before she received an automated call from Contra Costa County to remain indoors.
"I was feeling kind of nauseous and light-headed" from the smell, she told the newspaper.
The refinery produces gasoline, jet fuel, diesel fuel and lubricants, as well as chemicals used to manufacture many other products.
The blaze in the refinery's No. 4 Crude Unit was contained by 11 p.m. Monday, Chevron said in a statement on its website. Spokesman Nigel Hearne said the cause of the fire hasn't been determined and he wouldn't speculate on the cause.
Three employees suffered minor injuries and were treated at the scene, according to Kulp.
Randy Sawyer, the chief environmental and hazardous materials officer for the county's health services agency, said any kind of smoke can be toxic but added: "In this smoke, there can also be all kind of byproducts that can be toxic."
The agency had four teams of inspectors testing air quality, Sawyer said.
Trisha Asuncion, a hazardous materials specialist with the county, told the San Francisco Chronicle (http://bit.ly/MJRmhh) that no hazardous compounds had been detected in the air.
County health officials used automated calls to warn residents of Richmond, San Pablo and the unincorporated community of North Richmond to shelter in place, meaning they should not only stay inside, but should also turn off heaters, air conditioners and fans, and to cover cracks around doors with tape or damp towels.
Bay Area Rapid Transit also shut down three stations near the plant for several hours.
To the south, Oakland police issued a community advisory suggesting that residents of the North Oakland Hills area close all windows and doors and turn off air conditioners.
A fire at the refinery in January 2007 injured two workers and spewed low levels of sulfur dioxide and other toxins into the air. County officials said then that it was not enough to harm the health of nearby residents.
During an evening news conference, Hearne apologized "to the community for the fire and smoke this evening at the Richmond refinery."
The refinery is the largest producer of base oils on the West Coast, processing up to 240,000 barrels of crude oil a day, according to the company's website.
The company said Monday it did not know yet whether production would be affected. The 2007 fire shut down the refinery for most of that year's first earnings quarter.
The Associated Press contributed to this report.