Birdwatching is as popular in Japan as other countries. It is relaxing to go outside and observe birds in the nature being away from cities. Japanese cranes can be seen in Hokkaido.
Places you can go to observe birds around Tokyo:
Ueno Park
Meiji Jingu Shrine
Tokyo Yacho Koen (Wild Bird Park)
Places you can go in Hokkaido:
Akkeshi Waterfowl Observation Center
Tsurui-Ito Tancho (Red-crowned Crane) Sanctuary
Shunkunitai Nature Center
Place to observe birds in Kinki Region:
Osaka Nanko Bird Sanctuary
Hyogo Konotoi no Sato Koen (Stork Park)
If you are interested in visiting a bird museum in Japan, there is one. Abiko City Museum of Birdsis located in Abiko city, Chiba. To get the museum, take JR Joban line from Ueno to Abiko station.
Birdwatching will be a refreshing experience for you.
