The Pacific typhoon made its landfall in Chiba, northeast of Tokyo, around 5 a.m., according to the Japan Meteorological Agency.
Faxai is the 15th typhoon of the season and it recorded winds of 144 kmph and gusts of 216 kmph in the northeast direction and was moving towards the Pacific Ocean at 30 kmph after hitting the eastern coast of Honshu, the largest island on the Japanese archipelago, the Met agency said.
More than a dozen people were injured in Tateyama, while 10 more were hurt in Chiba, according to the Kyodo news agency.
According to state news agency NHK, some 930,000 households were left without power. Faxai also led to the cancellation of 138 flights earlier in the day and public transport services were heavily affected, Efe news said.
The East Japan Railway Company, also known as JR East one of the most important lines in the Tokyo metropolitan region have suspended operations but might resume later in the day.
The suspended lines made it difficult for the people living in Tokyo and its many suburbs to commute to their workplaces during the morning peak hours.
Bullet train operations were also affected, with the lines departing from Tokyo seeing several hours of disrupted service. The affected routes resumed their operations a few hours later.
As of 4.30 a.m., videos began to surface on social media of floodwaters inundating roads to apartment complexes.
"This will remain a compact storm during its lifespan," Senior Meteorologist Dave Houk said. Even though the storm is small in size, the threat should not be taken lightly especially near the coast of Honshu, including Tokyo as the rain and wind will be a threat to life and property, even though it will impact a relatively small area, according to Houk.
According to the Guardian, organisers of the Rugby World Cup are monitoring the cyclone and how it could impact or possibly cancel games set to take place in Tokyo over the weekend. This same time last year, a typhoon struck Kobe and Osaka, two cities that were hosting some rugby games of the World Cup.
( With inputs from IANS )