What is the main martial art in Japan?

The more systematic ones, such as karate, have many schools, such as Goken-ryu and Soto-ryu. There is also the famous Kyokushin Karate (not one of the four traditional karate schools, but a school that advocates combat)

Olympic sports such as Judo

Additionally, there is Kendo, Staff, Gun, Bow, and Cannon (Singijeon)

Additionally, there is the sometimes popular Aikido (which was developed from Guru-ryu Jiu-Jitsu, and includes Swordplay, Staff), Guru-Aikido (Battousai, and Yin-ryu Swordplay), and Ninjutsu.

Additionally, there is also ninjutsu (a comprehensive system, not in detail, mainly gunplay, swordplay, the use of some ninjutsu, and shuriken, in addition to the so-called five elements of the recluse, but definitely not as magical as in Naruto)

Additionally, there is also sumo wrestling. Personally though, I think that's just a sport.