JR East, the main suburban railway operator in greater Tokyo, has cancelled trains in the area to allow early morning track inspections for possible damage.
Non-compulsory evacuation orders were issued to more than 390,000 people across the Kanagawa, Shizuoka, and Tokyo prefectures.
Authorities warned it was risky to venture outside.
Language issues also sparked concern when a powerful typhoon hit Osaka and an natural disaster in Hokkaido triggered a prefecture-wide blackout past year, as both left many foreigners at a loss without sufficient information.
The Japan Meteorological Agencysays that "winds and rains could pick up suddenly, causing severe storms at sea, and there is a risk of record-breaking winds in the capital and other regions".
Around four to five typhoons make landfall in Japan every year, but it is unusual for them to do so near Tokyo. NHK said Faxai was the strongest storm in the Tokyo area in several years.
Winds were occasionally strong enough to shake street signs and buildings in Ichikawa early on Monday morning, while biting rain fell.
Photos taken on Monday morning show major subway stations rammed with commuters as the storm put a halt to bullet trains and underground services, all of which were shut down due to the high winds.
Traffic was snarled, schools were closed, and 5,000 people were ordered to evacuate their homes, many of them in the tourist city of Kamakura south of Tokyo, for fear of landslides.
The storm comes as Japan prepares to host the Rugby World Cup, which is expected to draw more than 400,000 overseas visitors.
They will now fly on to the coastal resort of Miyazaki later today, where they will be greeted with a welcome banner at the airport.
Ailments in the Japanese money guide to the Australia squad delaying their arrival by 24 hrs but, with getting escaped the worst of the climate, Eddie Jones' 31-man roster touched down on program.
North Korean state media urged citizens on Monday to "fully mobilize" to rebuild after powerful Typhoon Lingling lashed the country over the weekend, with workers rebuilding electricity networks, salvaging battered crops and helping families whose homes and property were damaged.
KCNA said the typhoon caused the destruction and flooding of 460 houses in North Korea.
The typhoon is now forecast to move northeast away from Japan and into the open Pacific over the next day, with maximum wind speeds expected to weaken to 26 miles per hour by Tuesday, according to JMA.
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