Japan is one of the 75 countries and territories which use left-hand traffic(LHT). Mostly other countries which use LHT are United Kingdom and most of its former colonies or current territories. Despite Thailand and Indonesia were never been the parts of British Empire, they follow LHT as same as Japan. Japan was never been a part of British Empire either.
It seems that LHT rule has already existed since 17th century. Samurai carried the sword on the left side of the body and it was better to follow left-hand traffic than right-hand traffic. If they followed RHT, their swords will hit others swords.
Although LHT, there are certain amount of left hand drive vehicle; driver sits in the left side of the vehicle as in continental Europe exist in Japan, all of the are imported vehicles; especially luxury cars. Therefore there are toll gates which are specially built for left hand drive vehicles. However, the number of these vehicles are reducing and more imported right hand drive vehilces, driver sitting on the right side are increasing.
Therefore major car rental companies offer only right hand drive vehicles in Japan. If you want to rent a car in Japan, you should watch several videos of LHT before your arrival!