Drone footage taken by NGO Agent Green showed fire at the refinery in the aftermath of the blast and black smoke rising from the area.
The crude oil plant is owned by Rompetrol Rafinare, part of KMG International Group.
Raed Arafat, head of the Department for Emergency Situations said firefighters were putting out the fire which should reduce the risk of further blasts.
Arafat said there have been "four victims, of whom one is missing. One has severe burns and two others have mild burns."