The fire broke out on Friday near the bundwall area and benzene containers. Television footage showed a large blaze and smoke rising from the refinery, which Pertamina said has 200 oil tanks and has a processing capacity of 348,000 barrels a day.
Pertamina official Djoko Priyono said in a statement that the fire had been extinguished on Sunday morning and a cooling process was underway.
"Everything is in a good condition and extinguished," he said, adding that supplies of LPG and fuel were not impacted.
A Pertamina spokesperson said that an internal investigation into the cause of the fire was being carried out.
This was the second recent fire at a Pertamina refinery after one in March at its facility in West Java.
(Reporting by Tabita Diela; Writing by Stanley Widianto; Editing by Robert Birsel)