The best way to reach Japan from India is via flights. Japan is well connected to India, and there are flights available from all major cities in India to Tokyo Japan. All flights from Delhi to Tokyo, Japan are direct and usually of a shorter duration. But flights from all other major international airports such as Chennai, Bangalore, Mumbai, Kolkata, and Cochin make a stopover at Delhi before continuing their onward Journey to Japan.
While flying out the duration of the flights is usually 35 hours or more because they are first directed to Delhi and have to bear long layovers. So, it would be best to make your arrangement to Delhi and then book a return flight from there to Japan. This way you would be able to save precious travel time and travel comfortably. If you don't mind the long connection, then you can always book flights from any of the city nearest to you.
The table below gives you an approx. The idea of time and flight duration, please not the price mentioned is a round-trip fare. One-way fares will vary and are usually higher. The lowest fare options are available from India's internationally carries, i.e., Air India. There are other airline options available as well Korean air, Singapore Airlines, Srilankan Airlines, Cathy Pacific and Malaysian Airlines. Unlike Air India, these airlines don't redirect to New Delhi but instead, have a layover in their home country. The travel time with these carriers are significantly shorter, but the prices are 10-15% more. So, in the end, you have to decide what it is you value more time or money. Because that is what will make your flight decision for you.
* Frequent flight names include Air India, Korean Air, Singapore Airlines,
Srilankan Airlines, Cathy Pacific, Malaysian Airlines
* Biggest Airport: Narita Airport, Tokyo, Japan.