By Yun Hwan Chae

SEOUL (Reuters) - Typhoon Chaba battered southern parts of South Korea with violent wind and heavy rain on Wednesday, killing at least three people and flooding the country's main port and industrial sites and disrupting production at some factories.

The storm hit the island of Jeju overnight and one person was reported missing amid widespread power outages and damage to homes and other buildings. Twenty-six flights linking the holiday island to the mainland and to China were canceled.

The port in the city of Busan was shut for a second day as Chaba whirled past and headed east towards Japan. An official at the country's biggest port said it was expected to reopen later in the day.

Work at Hyundai Motor's two factories in the city of Ulsan, which produce the Accent cars and Sante Fe sport utility vehicles, was suspended because of "inflow of water", a company spokeswoman said.

Operations were also suspended at some shipyards along the south coast, including at Daewoo Shipbuilding & Marine Engineering Co Ltd. in Geoje city, Yonhap news agency said.

Five people were killed in Busan and Ulsan, media reports said. The Ministry of Public Safety and Security put the death toll at three with three missing.

Television footage showed heavy flooding in parts of Ulsan and Busan, with cars and buildings partially submerged and storm-surge waves hitting apartment blocks near the coast.

More than 80 flights at the Gimhae Airport serving Busan were canceled, an airport official said. The KTX bullet train service in the south was also suspended.

Chaba was expected to weaken and was likely to be a tropical storm by the time it reaches Japan, according to the Tropical Storm Risk tracker service.

(Reporting by Jack Kim, Yun Hwan Chae, Hyunjoo Jin and Nataly Pak; Editing by Robert Birsel)