Initial indications ruled out environmental danger at the refinery in the industrialised bay of Izmit, run by Turkey's main oil refiner TUPRAS.
"Poisonous gas measurements are being made, but it seems at the moment that there is nothing negative," Ozdal said.
The explosion "appears to be a work of accident."
Cavit Aykanat, a representative of the local oil workers' trade union, told the Anatolia news agency that evacuations had begun as a precaution against a possible leak of poisonous gas.
Ambulances and fireighters were dispatched to the facility.