"Firefighters believe welding work at an underground restaurant might have caused the fire," a spokesman for the National Emergency Management Agency told AFP.
Most of the deaths and injuries at the terminal at Goyang, northwest of Seoul, were the result of smoke inhalation, he said.
The agency initially put the death toll at seven but revised it later, saying one victim had been revived by emergency treatment in hospital.
The five-storey terminal building has several bays that can station 250 buses, and a multiplex composed of a shopping centre, a supermarket and a movie theatre. Firefighters took about 30 minutes to bring the blaze under control.
As well as the ferry disaster in April, public confidence was shaken earlier this month by a subway train collision in Seoul that injured around 200 people.