The national weather bureau said the storm poses "a threat to all regions" across the island. The extreme weather phenomenon is forecast to hit China afterwards, where heavy downpours have killed over 180 people.
Taiwan's Defense Ministry on Thursday placed more than 30,000 troops on standby ahead of Super Typhoon Nepartak's landfall, which is expected overnight.
Nepartak, the first typhoon of the 2016 Pacific season, packed gusts up to 245 kilometers per hour (152 miles per hour) as it approached Taiwan's eastern counties of Hualien and Taitung.
"Its storm circle is gradually nearing southeastern Taiwan and the Hengchun peninsula, posing a threat to all regions and Penghu," the country's national weather bureau said.
More than 100 commercial and cargo flights were canceled at Taipei's two main airports. Maritime authorities ordered fishing boats to return to port as waves crested as high as 14 meters (46 feet).
At least 2,000 tourists have been evacuated from Green Island, a major Taiwanese tourist attraction.
The typhoon is set to dump torrential rains across the island, with mountainous areas expected to receive up to 600 millimeters (24 inches), prompting fears of possible landslides.
Typhoon Morakot in 2009 left more than 600 people dead, the majority of them buried in massive landslides.
After Taiwan, Typhoon Nepartak is forecast to hit China, where heavy downpours have caused flooded cities and villages in the past week.
At least 180 people have been killed or reported missing, according to the National Ministry of Civil Affairs.
Chinese President Xi Jinping ordered the deployment of army and police to disaster-hit areas. The floods forced nearly 170,000 people to relocate, with more than 80,000 having been placed in shelters.
Chinese paramilitary policemen were called in to pile up sandbags to reinforce the dyke of a river due to heavy rain in Xuancheng city
ls/sms (AFP, dpa)