Kochi no Ya Hostel is located in Aki, Kochi. It is a passion project of a towns local and offers one of the best hostels experiences in Japan.

Ichi the Hostel in Hiwasa in Shikoku is another hidden gem operated by a young entrepreneur. The hostel also has a pub attached to it.

The Hatchi Hostel in Kanazawa is operated by the Share Hotels. Central location, stylish cafe and immaculate facilities.

Kiyasato Ihatov Hostel located in Hokkaido is run by a couple and is in one of the most be- beautiful villages of Japan - Kiyasato. 

Yakushima is home to many accommodation options including hostels and South Island Hostel is one of the best options.

For more about Japan - you can visit my Japan based travel blog Bizarre Journeys. Do not limit yourself with Tokyo and Kyoto.