"This year was 1.97 degrees Celsius higher than usual... making it the hottest autumn since 1898, when statistics began," the Japan Meteorological Agency said Monday on their website.
Between September and November, the temperature was 2.4 degrees Celsius higher than usual in Tokyo, 2.9 more in the central city of Nagoya and 1.2 warmer in northern Sapporo city.
The weather has delayed the country's autumn foliage season -- when tourists flock to see leaves turn vibrant reds and yellows.
In Kyoto, a railway company known for running trains through forests of illuminated maple trees at night has extended its schedule because leaf colours are not changing as quickly as usual.
According to the Japan Meteorological Corporation, the best time to see the autumn leaves in Tokyo is around December 5 and in Osaka on December 9, both later than usual.
Japan recorded its joint-hottest summer on record this year as extreme heatwaves, which scientists say are fuelled by climate change, engulfed many parts of the world.
The famous snowcap of Mount Fuji was absent for the longest recorded period this year, not appearing until early November, compared with the average of early October.
Climate scientists forecast that 2024 will almost certainly be the hottest year on record.
Australia has meanwhile sweltered through its warmest spring on record, the country's weather bureau said Sunday, with temperatures 2.08 degrees Celsius above the average.
Australia's previous hottest spring -- running between September and November in the Southern Hemisphere -- was recorded in 2020.
