The storm is forecast to make landfall on the mountainous and sparsely populated east coast around 5pm AEDT on Thursday, according to Taiwan's Central Weather Administration, with strong winds and torrential rain affecting almost all the island.
Kong-rey slightly weakened overnight but remained powerful as the equivalent of a Category 4 hurricane packing gusts of more than 250km/h, according to Tropical Storm Risk.
Taiwan's weather administration labelled the storm a "strong typhoon", the most powerful storm level for Taiwan, adding it would be the biggest typhoon in size to hit the island since 1996.
Up to 1.2m of rainfall is expected in eastern Taiwan with destructive winds along coastal areas, according to the administration.
A fisherman secures his boat ahead of Typhoon Kong-rey at Pa-tou-tzu fishing harbour in Keelung. (AP PHOTO)
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.
Warnings for destructive winds of more than 160km/h were issued in the eastern county of Taitung.
The defence ministry has put 36,000 troops on standby to help with rescue efforts while 4500 people have been evacuated from high risk areas ahead of time, the government said.
Taiwan Semiconductor Manufacturing, the world's largest contract chipmaker and major supplier to companies like Apple and Nvidia, said that it has activated routine typhoon alert preparation procedures at all its factories and construction sites.
"We do not expect significant impact to our operations," it said in an emailed statement.
Taiwan's government has warned people to stay away from the mountains and the coast.
Kong-rey is forecast to weaken as it crosses the central part of Taiwan then move into the Taiwan Strait and graze China on Friday morning.
Subtropical Taiwan is frequently hit by typhoons. The last one, Typhoon Krathon, killed four people earlier this month as it passed through the south of the island.