The bus, which was stationary on a busy road at the time, was buried under the rubble of Guangzhou, about 270 kilometers (168 miles) southwest of the capital, Seoul.
Another 25 people were injured, including eight seriously, the ministry added.
The 16 demolition workers are safe and have not been injured as the building collapsed.
Approximately 190 firefighters were deployed for search and rescue, and police joined the rescue effort, the ministry said.
The cause of the collapse is unclear, Reuters reported, citing officials at the Guangzhou Fire and Security Headquarters. The Ministry of Land, Infrastructure and Transport will investigate the cause of the collapse.
South Korea is struggling with poor infrastructure safety indicators – the collapse of a department store killed more than 500 people in 1995, and the bridge in 1994 killed 49 people. In recent years, the country has tried to improve its safety record.