Mawar, which wreaked havoc on Guam earlier this week, has weakened to tropical storm strength from its earlier super typhoon status.
The main body of the storm was expected to pass south of the main island of Honshu as it moved into the Pacific, buy forecasters warned there was the danger that humid air from the storm could feed into a seasonal rain front, touching off heavy localised rains.
Nearly 1.3 million across Japan were advised to evacuate, the Fire and Disaster Management Agency said, with the largest number in areas of western Honshu such as Wakayama prefecture.
Just over 300 flights were cancelled as of noon on Friday, along with 52 ferries, the Transport Ministry said. A handful of train lines were also shut down.
Similar weather patterns have caused flooding and landslides in the past, most notably in the summer of 2018, when more than 200 people were killed in western Japan.
"What happened five years ago is still as clear as yesterday," one woman in the smallest main island of Shikoku told NHK public broadcaster, explaining why she had evacuated.
Television footage showed several rivers close to the top of their banks by mid-afternoon on Friday, but there had been no reports of flooding or landslides.
The JMA issued flood and landslide warnings for the western parts of Shikoku and Honshu islands, with forecasts of 350mm (13.8 inches) of rain in parts of western Honshu in the 24 hours up to Saturday morning.
Parts of Shikoku were hit by 162.5mm (6.4 inches) of rain in the three hours to 900 a.m. (2400 GMT), nearly half of that in one hour, NHK public broadcaster said.
Though heavy summer rains are not uncommon in Japan, June is unusually early for a typhoon-type storm to near the islands.
On Thursday, the Japan Meteorological Agency (JMA) said the nation had experienced its warmest spring since record-keeping began in 1898.