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A resident of Fujian province walks past a wall damaged by strong winds as Typhoon Fanapi hit Xiamen on Monday. ((Stringer/Reuters) )

Floods and landslides from the strongest storm to hit China this year have killed at least 54 people and left dozens missing, officials said Thursday.

Typhoon Fanapi swamped south China's Guangdong province after directly hitting the island of Taiwan on Sunday and killing two there. Guangdong's meteorological centre said heavy rains would start to ease Thursday night.

Fanapi had killed 54 and left 42 missing as of midday Thursday, said an official surnamed Zhou with Guangdong's flood control and drought relief headquarters.

The state-run Xinhua News Agency said earlier that the dead included five people who were killed when a dam at the Xinyi Yinyan Tin Mine in Xinyi city was hit by a landslide and collapsed.

The Civil Affairs Ministry estimated the typhoon has caused $12 million US in direct economic losses in Guangdong.

In southern Taiwan, two people died in flash flooding caused by Fanapi, which caused tens of millions of dollars of damage and dumped more than one metre of rain in some places.

Fanapi was the first major storm to strike Taiwan this year and the 11th typhoon to hit China. It had weakened significantly before landing in China's Fujian province.