The early morning fire sent plumes of black smoke over Yurakucho station gateway to the nearby luxury Ginza shopping area, where department stores were preparing for a rush to the New Year sales. (Agencies)
No casualties were reported but the blaze at commercial buildings, next to railway tracks near the station, forced the suspension of all bullet trains departing from the capital to the western commercial hubs of Nagoya and Osaka, a key section of the nationwide network, according to Central Japan Railway Company.
Bullet trains departing Osaka to Tokyo were also brought to a halt because the capital could not handle incoming services.
Thousands of passengers, many with children and clutching luggage, crammed onto platforms at the Tokyo station desperate for information, while others filled waiting areas and the main concourse. Some passengers sat on trains which were not moving.
The fire hit as families also began to return from holidays spent with family outside Tokyo and businesses and government services prepared to resume normal services from Monday after the New Year holiday.
The blaze was reported around 6:30 am (2130 GMT) and possibly started in a games arcade, according to Tokyo Fire Department, with more than 40 fire engines rushing to the scene.
It also stopped major commuter lines in Tokyo. Bullet train services to areas north of Tokyo were not affected.
Television footage showed the fire engulfing low-rise buildings which housed the games arcade and a pachinko pinball game parlour.
Smoke from the blaze sent a haze over the Yurakucho business and shopping district next to Ginza.
Fashion boutiques and department stores sent emergency tweets to announce delays to their opening hours, as emergency crews battled the fire.
Bullet trains had resumed by midday (0300 GMT) but the rail system remained congested.
The early morning fire sent plumes of black smoke over Yurakucho station gateway to the nearby luxury Ginza shopping area, where department stores were preparing for a rush to the New Year sales.