"The bodies of the four victims have been found," said an official from the National Fire Agency, which coordinates rescue operations in Taiwan.
A 60-year-old man was drowned in northern Hsinchu city.
Two agricultural officials were found dead after they were washed away by rising floodwater outside the city in Hsinchu county.
The fourth victim was working on a riverbed in southeastern Taitung county when he was engulfed by floodwaters, the agency said.
Hundreds of residents were evacuated from Hsinchu county and central Nantou, where at least 500 millimeters (20 inches) of rain had fallen in three days, it said.
"They were relocated to nearby places which are safe," Hsinchu's deputy council magistrate Peng Kwang-cheng said.
Television footage showed two cities outside Taipei -- Sanchung and Hsinchuang -- were marooned, with flood rising to three meters in some places.
Taiwanese authorities also ordered the hundreds of people to be evacuated from mountainous regions where the torrents of water were causing landslides.
The downpours prompted landslide alerts in six counties and a city, interrupting the search for three people who went missing and were feared killed in a landslide while scaling a mountain in Nantou on Tuesday.
Another man, a worker on a bridge in Hsinchu county, was washed away by rising floods, but is still listed as missing.