Born in 1887, Hongo was recognized as the world's oldest by the Guinness Book of Records after an American woman Maude Farris-Luse died in March at the age of 115.
Her doctor, Kiyoshige Niina, said she died of pneumonia.
Hongo was famous throughout Japan for her habit of sleeping for two days and then staying awake for two days.
She had been hospitalized in Kagoshima, on the southern island of Kyushu on Oct. 8, after complaining of loss of appetite and fever. She appeared to have been recovering when her condition worsened Friday, Niina told a news conference.
Raised on a small, rural island on Japan's southern fringe, Hongo grew up tending cows and farming potatoes. The same island also produced the Japanese record-holder for longevity, a man, Shigechiyo Izumi, who died in 1986 at the age of 120.
Hongo's death comes a little more than a month after the man believed to be the world's oldest also died in Japan.
Yukichi Chuganji, a retired silkworm breeder, died at his home in late September at age 114.
Chuganji was born March 23, 1889 in the farming town of Chikushino also on Japan's southernmost main island of Kyushu.
Hongo and Chuganji's deaths symbolized the graying of Japan's society a trend that elicits both pride and concern.
There are an estimated 20,000 Japanese over the age of 100, and women make up about 80 percent of the total.
Japan's life expectancy is the longest in the world for both sexes — 85.23 years for women and 78.32 for men in 2002. The country's traditional fish-based, low-fat diet may be the secret to the long lives, researchers say.
An annual government survey released this year in conjunction with Respect for the Aged Day, a national holiday, showed a record 24.3 million Japanese almost one in five have reached their 65th birthday.
At the same time, Japan marked a record low 1.32 births per woman last year, a figure that been falling for the last three decades and reflects changing values that have led more women to choose careers over children.
The changing demographic has raised fears the nation's pension and health care systems will be badly strained in the years ahead by a population consisting of fewer people of working and taxpaying age.
It was not immediately clear who the world's oldest person was following Hongo's death. Japan's Health, Labor and Welfare Ministry said Mitoyo Kawate of Hiroshima 114 years old became the oldest person in this country.