More than 70 consoles have been confiscated from incoming travellers in the past four days because they are not licensed for use in the country, local media reported.
A disgruntled engineer who purchased a Wii abroad told local TV station TVBS News how his brand new console was seized by customs officials when he returned to Taiwan.
"They told me if they check with the X-ray machine and discover a Wii, then it's game over. They take the machine, the controller, and the game CDs, and confiscate them all," he said.
While much of the world already has access to the popular console, Taiwan must wait for radio emissions testing to be complete before the Wii can be sold legally.
The console uses Bluetooth wireless networking, which must be officially tested in a local lab and certified by Taiwan's regulatory authorities.
Customs authorities initially told Wii owners that they would have to apply for a special import permit from communications authorities, and then take the machines to be tested themselves.
This is normally a lengthy and complex procedure taking months and costing about $100, TVBS estimated.
Officials say they have tried to make things easier by providing application forms at the airport, but it is still unclear how long it takes to process the applications.
A thriving online black market in Wii consoles has sprung up in Taiwan.