Previous reports said eight people were injured in the blast.
Jovicic said the refinery has continued operating after the incident, adding that an investigation, which was still underway, should establish the cause of the explosion.
The Brod refinery, which processes 1.2 million tonnes of crude a year, is majority owned by Russia's Neftegazinkor, a unit of state-owned oil company Zarubezhneft.
Auditors have warned that it may face liquidity problems after it piled up losses and its liabilities exceeded assets. The company, however, has dismissed those claims.
Citizens of nearby Slavonski Brod just across the border in Croatia have complained about rising pollution levels from the refinery for years and Bosnian and Croatian authorities have been working to combat this issue.
Air quality measures showed no major spike in pollution levels on Wednesday, Jovicic said.
(With inputs from agencies.)