In Kanagawa prefecture, south of Tokyo, helicopters were being used to look for two elementary school boys who were believed to have been near a beach during the storm, a police spokesman said.
And fears were growing for the safety of a man in his 50s in Chiba prefecture, who has been missing since telling police there had been a landslide behind his house.
At a train station east of Tokyo, a large landslide underneath the track left sleepers exposed, a spokeswoman for Keisei Electric Railway said.
The Keisei line is one of the major rail access ways to the busy Narita Airport, the main international gateway to Tokyo.
More than 400 flights to and from Tokyo have been cancelled, most of them domestic, according to major Japanese airlines All Nippon Airways and Japan Airlines.
Two flights between Tokyo and Seoul and another two flights between Tokyo and Hong Kong were among the cancellations, ANA said.
Altogether, the cancellations affected plans of some 61,600 travellers, the airlines said.
Further north, the operator of the battered Fukushima nuclear plant said it had released some rain water that was trapped inside its barrages, but added that its radiation reading was within safety limits.
It reported no ill effects on the power station, where thousands of tonnes of radiation polluted water are being stored in tanks after being used to cool reactors.
Typhoon Wipha, which had not made landfall, brought heavy rains and strong winds to Tokyo’s metropolitan area, heavily disrupting the morning commute for hundreds of thousands of people.
At 0100 GMT, it was located in the Pacific some 160 kilometres (99 miles) east of Koriyama in Fukushima prefecture, according to the Japan Meteorological Agency.
It was moving northeast, gradually shifting away from Japan, the agency said.