Other trains operated at only partial capacity, filled with stoic office workers clutching umbrellas.
"It's indeed scary, the wind and everything," said Misuzu Susaki, who braved the storm. "It's incredible."
Evacuation advisories were issued to thousands in the vicinity of the capital. Wipha had been billed as a once-in-a-decade typhoon but, aside from some flooded streets, there were few reports of significant damage.
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The storm was 40 km (24 miles) east of the city of Katsuura and moving northeast at 65 kmh by 7:00 a.m. (2300 GMT). It carried sustained winds at its center of 126 kph (78 mph) and gusts up to 180 kph (112 mph), the Japan Meteorological Agency said on its website. It was expected to weaken into a tropical depression later on Wednesday.
Trees were toppled and several houses swept away by landslides on Izu Oshima island, where some 800 mm of rain was recorded in the 24 hours up to Wednesday morning - more than twice the usual monthly rainfall for October.
Domestic and international flights at Tokyo's Haneda and Narita airports were cancelled, and several subway lines in the city stopped running due to the high winds. Thousands of schools closed as a precaution.
The typhoon was expected to pass near the crippled Fukushima plant, on the coast 220 km (130 miles) north of Tokyo, later on Wednesday.
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The operator of the plant, Tokyo Electric Power, which has been struggling to contain radioactive leaks, said it would cancel all offshore work and would decide whether to continue work onshore after assessing the weather.
It was pumping out rainwater at the tanks storing radioactive water, a by-product of a jerry-rigged cooling system designed to keep under control reactors wrecked in a 2011 earthquake and tsunami.
The rainwater will be pumped into an empty tank, checked for radioactivity and, if uncontaminated, released into the sea, the company said.