The country's centenarian population jumped by 4,423 from a year earlier to a record 58,820 as of September 1, the health ministry said, adding that 87.1 per cent of them were women.
On average, there are 46.21 centenarians per 100,000 people.
The figures included the world's oldest woman and her male counterpart, as recognised by Guinness World Records -- Misao Okawa, a 116-year-old woman in Osaka, and Sakari Momoi, the oldest known man at 111.
"Progress in medical technology and an improvement in the care-giving system may have contributed to the steady rise," said ministry official Yuji Umemoto.
In 2013, life expectancy for women in Japan was 86.61, the longest in the world, while for men it was 80.21, the fourth longest, the ministry said earlier.