The storm hit the mountainous and sparsely populated east coast on Thursday afternoon between Taitung and Hualien counties, according to Taiwan's Central Weather Administration, with strong winds and torrential rain affecting almost all the island.
At one point a super typhoon, Kong-rey slightly weakened overnight but remained powerful as the equivalent of a category-four hurricane packing gusts of more than 250km/h, according to Tropical Storm Risk.
Strong winds and torrential rain are affecting almost all the island of Taiwan. (AP PHOTO)
Taiwan's weather administration said it would be the biggest typhoon in size to hit the island since 1996.
"I hope that everyone in the country will co-operate in avoiding disaster and refraining from engaging in dangerous behaviour such as wave watching during the typhoon," President Lai Ching-te wrote on his Facebook page.
Administration forecaster Gene Huang said after hitting the east coast it would head towards the Taiwan Strait as a much-weakened storm and urged people across the island to stay at home due to the danger of high winds.
"The size of the storm is very large and the winds are high," he said.
Environmental officials were working on Thursday to prevent oil leaking from a Chinese cargo ship beached against rocks on Taiwan's northern coast after losing power in turbulent weather.
Warnings for destructive winds of more than 160km/h were issued in the eastern county of Taitung, whose outlying Lanyu island recorded gusts above 260km/h before some of the wind barometers there went offline.
Up to 1.2 metres of rainfall is expected in eastern Taiwan as well as destructive winds along coastal areas.
"The size of (Kong-rey) is very large and the winds are high," a forecaster said. (AP PHOTO)
The defence ministry has put 36,000 troops on standby to help with rescue efforts while 1300 people have been moved from high-risk areas.
Taiwan Semiconductor Manufacturing Co, the world's largest contract chipmaker and major supplier to companies such as Apple and Nvidia, said it did "not expect significant impact to our operations".
Taiwan's transport ministry said 298 international flights had been cancelled, along with all domestic flights and 139 ferry services to and from outlying islands.
Taiwan's high-speed railway, which connects major cities on its populated western plains, continued to operate with a much-reduced service.
In the capital, Taipei, the city government said overground parts of the subway system had stopped operations because the wind was too strong.
Kong-rey is forecast to graze China along the coast of Fujian province on Friday morning.
Subtropical Taiwan is frequently hit by typhoons.
The last one, Typhoon Krathon, killed four people earlier in October as it passed through the south of the island.
