The warning is issued only when it forecasts conditions seen once in several decades.
Some fights have been cancelled and bullet train services delayed, with rainfall expected to worsen in Tokyo and areas north of Tokyo later in the day.
It was one of the strongest temblors to rock Tokyo since the massive 9.0 earthquake and tsunami disaster in 2011 that killed thousands.
More than 140 people suffered mostly minor injures, many of them by falling objects and cuts while stepping on broken glass.
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