Shigetaka died on Sunday at a hospital near his hometown in Hiroshima, prefectural (state) spokesman Shinichi Yokota said.
A farmer from Hiroshima, Shigetaka became the nation's oldest Japanese man in July 2004.
Japan's oldest man is now Nijiro Tokuda of Kagoshima, southern Japan, who is just one month younger, Yokota said.
The nation's oldest person is a 112-year-old woman _ Yone Minagawa of Fukuoka, also in southern Japan, born in January, 1893, according to the Health Ministry.
Shigetaka used to enjoy watching samurai dramas on TV and eating sashimi and eel. He had been hospitalized over the last two years and spent most of his final days in bed.
The oldest living man is Emiliano Mercado Del Toro, 113, of Isabela, Puerto Rico, according to Guinness World Records.
Japan has one of the world's longest average life spans. In 2003, Japanese women set a new record for life expectancy, at 85.3 years, while men live an average of 78.3 years.
Experts say a traditional fish-based, lowfat diet may be Japan's secret to long life.