Concrete from the collapsed building in the southern city of Gwangju fell on the bus carrying 17 people that had stopped on a nearby street, the National Fire Agency said.
Emergency officers dispatched to the scene rescued eight people from the bus, all seriously injured, before discovering the nine bodies, the agency said in a statement.
Fire officer Kim Seok-sun said in a televised briefing from the site that all workers at the construction site had been evacuated prior to its collapse. He said some of the workers told investigators they had closed a pedestrian walkway near the building before the collapse.
Fire agency officials said emergency officials were still searching for other people who may be trapped under the rubble. The cause of the collapse was not immediately known.
Kim said the bus driver was among those injured. Authorities did not immediately provide details of the other people injured or killed.
An earlier statement from the fire agency said debris also fell on two passenger vehicles. But agency officials later corrected that after watching security videos.
Local media showed debris falling on the bus and enveloping the street in a huge cloud of dust. Video after the collapse showed dozens of rescuers equipped with stretchers and crowbars searching for survivors as bulldozers cut through a massive mountain of crumbling concrete and bent steel girders that spilled onto the highway.