You can get in to Japan by plane and even by boat.
Narita Airport, Osaka International Airport, Kansai Airport and Haneda Airport of Tokyo are the major airports of Japan. Ibaraki Airport, north of Tokyo, also sees a number of flights landing and taking off. The major carriers of Japan are All Nippon Airways and Japan Airlines. You can also fly in via Seoul on Korean Air or Asiana Airlines. Delta Air Lines, United Airlines, and American Airlines have flights catering to many destinations in the US and Asia.
International ferry services to Japan are available, from Korea, China, Taiwan and Russia. Busan-Osaka, Shanghai-Osaka/Kobe, Keelung-Ishigaki/Naha and Russia to Japan via Sakhalin are some of the major ferries.
The airlines that go from India to Japan are Jet Airways, Air India, Korean Air, Singapore Airlines, Emirates, Jet Star, Cathay Pacific and China Airlines. There aren't any non-stops. The most common ones are 1 stops or 2 stops.