Typhoon Shanshan was moving towards the southern Amami archipelago, packing gusts of up to 216 kilometres (135 miles) per hour.
Heavy rain prompted the suspension of the bullet train between the central cities of Hamamatsu and Toyohashi, with services resuming at 09:15 am (0015 GMT), according to the operator.
There were also delays on other parts of the high-speed network and local trains, Central Japan Railway and West Japan Railway operators said.
Japan Airlines said it will cancel 116 domestic flights Tuesday and Wednesday, as well as six international flights.
The Japan Meteorological Agency urged residents to "evacuate from dangerous places", as it warned of heavy rain and potential landslides in the central Shizuoka area and high waves hitting the southern Amami region.
Typhoon Shanshan is expected to veer towards the main southern island of Kyushu later this week.
It comes in the wake of Typhoon Ampil, which disrupted hundreds of flights and trains this month.
Despite dumping heavy rain, it caused only minor injuries and damage as it churned up the Pacific coast past the Tokyo region.
That system came days after Tropical Storm Maria brought record rains to northern areas of Japan.
Typhoons in the region have been forming closer to coastlines, intensifying more rapidly and lasting longer over land due to climate change, according to a study released last month.
kh/rsc
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