The typhoon first struck Japan in the Kanagawa prefecture (state) to the southwest of Tokyo, before moving northwards and losing strength. By Friday afternoon, it was around 300 kilometers (180 miles) northeast of the capital, with winds of 108 kph (66 mph), the Japan Meteorological Agency said.
An elderly man was killed by a falling tree, and a construction worker perished when he was trapped in landslide at a dam construction site, Japan's Kyodo news agency reported.
Several houses were completely destroyed, and hundreds damaged by floodwaters. Evacuation warnings were given in many areas, and flights were cancelled due to high winds at airports across the country, including eight international flights at Narita airport near Tokyo.
The agency reported that although power has been restored to districts, many thousands of homes in eight prefectures across the country are currently without electricity.
Police also announced that a 52-year-old man had gone missing Thursday after "going to have a look at the swollen river." He is believed to have been swept away by floodwaters.
Typhoon Usagi (Rabbit) hit southern Japan last month, spreading chaos and causing injuries. Typhoon Fitow is named after a flower found in Micronesia, a group of Pacific islands.
Asian names for typhoons have been submitted for use by countries affected in the Asian Pacific area since 2000. When the list of 140 typhoons is exhausted, it reverts to the first name. The names of especially destructive or powerful typhoons are, however, removed from the list.