The figures further highlight the slow-burning demographic crisis gripping the world's fourth-biggest economy as its population ages and shrinks.
As of September 1, Japan had 95,119 centenarians, up 2,980 year-on-year, with 83,958 of them women and 11,161 men, the health ministry said in a statement.
On Sunday separate government data showed that the number of over-65s has hit a record high of 36.25 million, accounting for 29.3 percent of Japan's population.
The proportion puts Japan at the top of a list of 200 countries and regions with a population of over 100,000 people, the Ministry of Internal Affairs and Communications said.
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