Japanese officials said Kirishima died at the age of 70 at a hospital in Kanagawa Prefecture, south of Tokyo.
The fugitive was arrested last week after allegedly being involved in a series of bomb attacks against major Japanese companies in 1974 and 1975, including Mitsubishi Heavy Industries and Mitsui.
Kirishima has been wanted ever since, with his picture posted on search panels at police stations in Japan.
Before dying, the fugitive identified himself and revealed that he had worked as a construction contractor for years under a false name in a prefecture near Tokyo.
The fugitive was a member of the East Asia Anti-Japanese Armed Front (Eaajaf), a Japanese far-left terrorist organization of an anarchist nature that operated between 1972 and 1975.
The 1974 incident at Mitsubishi Heavy Industries is one of the most notable because it was done in broad daylight, killing eight and injuring 165.
Kirishima was responsible for the 1975 home-made explosive detonation of the Korea Industrial Economic Research Institute in Tokyo's central Ginza district.
The group, which carried out 12 such attacks in a row, was disbanded after authorities detained most of its members, many of whom were linked to or affiliated with the communist group the Japanese Red Army.
So far, eight Eaajaf members have been formally charged, two of whom have been sentenced to death.
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