The fire raged Wednesday through the second floor of the cargo warehouse belonging to Kerry Logistics Company, in Guanyin District in western Taoyuan City at around 10 a.m.
Some eyewitnesses said they heard an explosion before the blaze, the Central News Agency reported.
Hundreds of firefighters were dispatched to the scene and two Vietnamese migrant workers were pulled out, according to the local fire department.
A 30-year-old migrant worker was pronounced dead after being taken to a nearby hospital while another worker in his 30s was badly injured.
Two other Vietnamese workers were declared missing and their bodies were only found a day later.
Initial information is that some flammable alcohol was being stored on the second floor might have ignited the blaze, but authorities have not confirmed anything.
The disaster follows a string of recent accidents in Taiwanese factories, raising questions about safety standards in Taiwan.
In April last year, seven people, five firefighters and two workers from Thailand, lost their lives in an electronics factory fire in northern Taiwan.