Tanaka, who was born on January 2, 1903, died on April 19, the ministry said.
Guinness World Records said they were saddened to hear of Tanaka's passing, and said the news of her death had been confirmed by senior gerontology consultant Robert Young, who also helped confirm her record as the oldest person alive back in 2019.
Tweeting about her death, Guinness World Records said: "She became the oldest living person in January 2019 at the age of 116 years and 28 days.
"She is also the second oldest person ever recorded, behind only Jeanne Calment who lived to the age of 122."
Tanaka's family said in a tweet earlier this month that she had been frequently sick recently and "in and out of hospital."
Born in 1903, Tanaka married a rice shop owner at the age of 19, and worked in the family store until she was 103.
She twice survived cancer and lived through a multitude of historical events, surviving two world wars and the 1918 Spanish flu -- as well as the Covid-19 pandemic.
CNN previously reported on Tanaka during her preparation to participate in the Olympic torch relay ahead of the postponed Tokyo 2020 Summer Olympics.
The plan had been that she would take the flame as it passed through Shime, in her home prefecture of Fukuoka, but ultimately she did not participate, because of concerns about Covid-19.
Tanaka had been living in a nursing home in Fukuoka. Her family said she kept her mind and body engaged by doing math and remaining curious.
Tanaka's great-granddaughter Junko Tanaka set up a Twitter account in January 2020 to celebrate the supercentenarian's life.
She tweeted photos of her great-grandmother enjoying treats such as cake and soda pop, and shared her achievements and the exchanges she had with her relatives.
CNN previously reported Junko as saying of her grandmother: "I might be biased because I'm related to her but I think it's kind of amazing -- I wanted to share that with the world and for people to feel inspired and to feel her joy."
In 2020, one in every 1,565 people in Japan was over 100 years old -- more than 88% of them women. Government figures released in July 2020 showed that women have a life expectancy of 87.45 years compared with 81.4 for men.
Announcing Tanaka's death on its website on Monday, Guinness World Records said "the titles of oldest person living and oldest person living (female) are currently being investigated" and that further details would be announced in due course.