The explosion of recreational activities such as mountaineering in the early twentieth century provided the spur to the creation of Japan's first national parks in 1931 . Indeed, the Physical Fitness Bureau controlled the twelve newly established national parks until the military started using them for manoeuvres in the war years. The Environment Agency , formed in 1971 and upgraded to a ministry in January 2001, is officially responsible for the national parks and protection of the country's flora and fauna in general, though its scope and successes have been limited.

Endangered species , of which there are 206, are listed in the Red Data Book of Japan , which was compiled in 1991 due to direct threats to population numbers from hunting, habitat degradation and environmental pollution. The list includes the Iriomote wild cat ( Felis iriomotensis ), endemic to Okinawa's Iriomote-jima , of which only an estimated one hundred remain, the short-tailed albatross ( Diomedea albatrus ) and the Japanese otter ( Lupus lupus ) of Shikoku, both of which were once thought to be extinct. Recently, an animal very similar to a Japanese wolf, thought to have been extinct in 1905, was photographed in central Kyushu.

Conservation efforts come in the form of breeding and feeding programmes, habitat improvement and research projects. In an example of Russo-Japanese co-operation, researchers from both countries attached transmitters to fourteen sea eagles and tracked them by satellite to discover their migratory routes and feeding grounds. Unfortunately, however, many such conservation programmes fall far short of their goals largely due to an ineffective government system. According to the Mammalogical Society of Japan, over half of the endangered mammals on the list are close to extinction.

At a grass roots level, volunteer groups and Non-Governmental Organizations (NGOs) play a key role both in campaigning and in carrying out government projects, one arena in Japan where women are extremely active. These programmes have brought some success. The Japanese crane ( Grus japonensis ), a magnificent tall-standing bird highly celebrated in Japan for its grace and beauty and as a symbol of longevity, has benefited from volunteer-based feeding programmes in the Shiretoko region of Hokkaido. As a result, the numbers have increased from a mere 33 birds in the 1950s to a stable population of around six hundred today. Ironically, the Japanese crane is one of the birds most commonly seen in Japan - on the back of the thousand yen note.