Nonaka's family has run a hot springs inn for four generations.
Born on July 25 1905, Mr Nonaka grew up in a large family and followed his parents in running the inn, which is now run by his granddaughter.
The world's oldest man has died at the age of 113.
Nonaka's family noticed on Sunday morning that he wasn't breathing. He enjoyed eating something sweet after a meal, watching TV, reading newspapers, and soaking in a hot spring once a week in his late years, according to his family.
Nonaka had outlived all of his siblings as well as two of the five children he had with his wife, who died in 1992.
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His granddaughter Yuko said Nonaka didn't have any health issues - he just passed away peacefully. Nonaka died at the age of 113 on Monday, local media reported.
In retirement, he enjoyed watching sumo wrestling on TV and eating candies, according to local media.
The fastest-aging country in the world, Japan as of September 2018 had a centenarian population of 69,785, almost 90 percent of them women, according to the Ministry of Health, Labor and Welfare.
At the time of being confirmed the world's oldest man by Guinness World Records in April previous year, Mr Nonaka was still able to move around by himself in a wheelchair.
The oldest verified person - the French woman Jeanne Louise Calment - died in 1997 at the age of 122, according to Guinness World Records.