"Eight of them were brought to the hospital. One died on admission while another remains critical," said Dr Anil Jasinghe of the Colombo National Hospital.
While another person died at a nearby medical centre.
The 50,000 a day barrel capacity refinery at Sapugaskanda, a Colombo north suburb, had only resumed its operations last week having been shut for over two weeks over non availability of Iranian crude.
The refinery is only geared to handle Iranian crude.