Three people have been killed and thousands evacuated in several days of rainstorms in southern China, flooding major cities and affecting air and rail transport, authorities said Monday.

Pictures showed widespread inundations in the boom town of Shenzhen, in Guangdong province, with the brown waters several inches deep. Cars were seen stranded in expanses of water, and pedestrians waded through ankle-deep floods.

Meteorological authorities said it was the biggest storm to hit the city since 2008, according to state media reports.

Nearby Hong Kong was also inundated, causing travel chaos in the Asian financial hub with flights grounded and trains to the mainland cancelled.

The torrential rain soaked the region from Thursday, China's Ministry of Civil Affairs said in a statement.

By early Monday, three people had died and 29,000 had been evacuated in the five provinces of Jiangxi, Hunan, Guangdong, Guangxi and Guizhou, the ministry said.

More than 10,000 houses collapsed or were damaged and 9,000 hectares (22,000 acres) of farmland will yield no harvest, it said, estimating economic loses at 930 million yuan ($149 million).