She succumbed to heart and kidney problems resulting from pneumonia at the municipal hospital in the Japanese city of Kagoshima, some 950 km southwest of Tokyo.
"As a sort of farewell, she performed her favourite hand dance yesterday while lying in bed before her next of kin. She knew that her time was near," her 47-year-old grandson Tsuyoshi Kurauchi said.
Witness to three centuries
Guinness World Records named Hongo the oldest person in the world in March 2002, following the death of the previous record-holder Maude Farris-Luse of the United States at the age of 115.
Hongo, famous for her habit of sleeping two days in a row and then staying awake for the next two, was admitted to the hospital with a fever three weeks ago.
She was witness to three different centuries in her unusually long life.
According to her official register, Hongo was born on 16 September, 1887.
"She built up her body by working in a sugarcane field in her youth. Her strong vitality was the secret of her long life," Hongo's third daughter Shizue Kurauchi, 79, said.
Hongo gave birth to four sons and three daughters from her marriage in 1914.
Her children, grand-children, great-grand-children and great-great-grand-children totalled an astonishing 140.
Japan is famous for the longevity of its people.
Japanese women enjoy the highest average life-expectancy in the world of 85.23 years.
Japanese men have an average lifespan of 78.32 years.