No injuries were reported after the fire that began in one building and spread to three other structures, the Yomiuri Shimbun reported.
Helicopters joined dozens of firetrucks and other vehicles in the firefighting operation, officials said.
The Keihin-Tohoku and Tokaido lines were partially suspended because of the fire, transportation officials said.
A total of 125 train trips were canceled, affecting 270,000 people.
Bullet-train services affected by the fire were resumed before noon, Kyodo reported.
The fire also burned the transmission lines of East Japan Railway Co.