The storm, described by the official Xinhua news agency as the world's strongest typhoon this year and the worst to hit Fujian province since records began in 1949, had killed seven people by Friday morning, the civil affairs ministry said in a statement.
Another nine people were missing and more than 330,000 residents had been relocated, it added.
The typhoon, which had earlier skirted the southern tip of Taiwan, made landfall in Xiamen early Thursday packing winds of around 170 kilometres per hour (105 miles per hour) and bringing downpours across the province, said the statement.
Flooding destroyed an 871-year-old bridge that was a protected heritage site in Yongchun county, Xinhua reported Friday.
Sinking fishing vessels caused by super typhoon Meranti in Kaohsiung city, southern Taiwan, 15 September 2016 (AAP) Source: AAP
At one point more than 3.2 million homes had their electricity cut off and water supplies for many communities in Xiamen were disrupted, it added.
The storm had weakened to a tropical depression on Friday.
Fresh warnings
The country has issued a landfall warning for Typhoon Malakas, which is expected to bring strong winds to the eastern and northern parts of the country.
As the cleanup from Meranti continues, Malakas is expected to sweep north off the eastern coast of Taiwan before turning northeast toward Japan, the state-run Central News Agency quoted the Central Weather Bureau as saying.
The eye of the storm was located about 470 kilometres to the southeast of Taiwan and was moving northwest at a speed of 22 kilometres per hour, according to the bureau.
"Residents in eastern Taiwan should stay alert to strong winds and heavy rain.
A handout satellilte image made available by the Central Weather Bureau shows the movement of Typhoon Malakas (AAP) Source: AAP
Typhoon Malakas is possibly getting stronger," Bureau forecaster Wu Wan-hua told a news conference Friday.
The Japan Meteorological Agency is also warning of strong winds and high waves around islands in the southern Japanese archipelago, saying the typhoon could produce waves of up to 11 metres in the region.
The agency expectsthe typhoon to be around 60 kilometres south of Yonaguni Island at 9 am on Saturday.
