Jiroemon Kimura, who was born in 1897, died in hospital early today morning "from old age", an official in Kyoto's Kyotango city said in a statement.
Kimura, who was from Kyotango, was hospitalised in early May suffering from pneumonia. A few days ago doctors noted that his condition was worsening.
Kimura was recognised by Guinness World Records as the world's oldest living person in December 2012, after a woman from the United States died at the age of 115.
However, he was well off the all-time record set by French woman Jeanne Calment, who died in 1997 at the age of 122, making her the longest living person in history.
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Kimura, who was born the same year as American aviation pioneer Amelia Earhart, celebrated his 116th birthday in April, receiving a pre-recorded video greeting from Japan's Prime Minister Shinzo Abe.
The centenarian had seven children, 14 grandchildren, 25 great-grand children and 15 great-great grandchildren, and worked at a post office for about 40 years. After retiring he took up farming which he continued to do until the age of 90.
Kimura's motto in life was "to eat light and live long," the official added.
The mayor of Kyotango will pay his respects at Kimura's house while the city hall will prepare a place for a book of condolences, the official said.
"I heard a wake will be tomorrow and a funeral the day after tomorrow," he said.
"Mr. Kimura was popular among residents so we expect many people to visit to sign condolences," he added.
Encouraged by Kimura and 94 other people in Kyotango who will this year be 100 years old or more, the 60,000-strong city, together with 36 other municipalities, is planning to launch a research project to examine their diets and find the secrets of their longevity.