Downgraded from a typhoon, Lan roared in from the Pacific at around 5 am (2000 GMT), soaking and buffeting with strong winds the commercial hubs of Osaka and Kobe as it rumbled northwards.
"Total rainfall has already exceeded the normal monthly rainfall for August in some places" in central and western regions, the Japan Meteorological Agency said on the social media platform X.
"Please be cautious of heavy rain... and very strong wind," it warned.
Electricity was mostly restored in seven regions, but 15,600 households were still without power as of Tuesday afternoon, according to a local utility.
Part of a pedestrian bridge was swept away in Kyoto and flying debris stopped local commuter trains.
Express bullet trains were suspended as planned along with hundreds of flights, including 240 Japan Airline services and 313 of rival ANA, particularly those serving Osaka.
Around 650 people were forced to stay overnight at Kansai airport, located on an artificial island in Osaka Bay, after rail and road access was cut off by the storm, Kyodo News reported.
Local governments issued non-compulsory evacuation instructions to more than 237,000 residents, especially in Wakayama, Kyoto and the ancient capital of Nara.
A town in Hyogo region issued the top-level warning to its nearly 16,000 residents, asking them to "take action to save lives" and "evacuate to higher places" as a river was flooding.
The weather system was forecast to spend all of Tuesday sweeping over the region, before moving out to the Sea of Japan and sweeping up the coast past Vladivostok and the Russian Far East.
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