The fire at the Pulau Bukom refinery, about five kilometres southwest from Singapore's mainland, started Wednesday afternoon and flared up again in the evening.
Some company firefighters suffered heat exhaustion and minor injuries, but "no one was seriously hurt," Shell said in a statement.
All staff were accounted for and non-essential staff had been evacuated, it added.
Shell said the fire had been contained within an area of approximately 150 metres by 50 metres.
"We believe it was an accident," the statement said.
The Bukom site is Shell's largest refinery globally in terms of crude distillation capacity with 500,000 barrels per day, according to the company website.
It said 90 per cent of Bukom's products were exported to countries in the Asia Pacific region and beyond.