Of the 40,399 centenarians, 87 percent are women, the Health and Welfare Ministry said.
An ageing population that is also forecast to shrink is among the challenges facing new prime minister Yukio Hatoyama and his Democratic Party, elected in a landslide last month.
A smaller workforce will have to shoulder the burden of ballooning pension and healthcare requirements. Just over three people of working age now support each elderly person, but in 50 years the ratio will be closer to one to one.
Hatoyama's Democrats have pledged to standardise the pension system with a minimum of 70,000 yen ($765) per month for those who had low incomes or lacked sufficient contributions to qualify for a pension.
Japan's centenarian numbers rank it second in the world behind the United States, which now has more than 96,000, according to U.S. Census Bureau estimates. But the U.S. population is more than double that of Japan.
Japan boasts the longest life expectancy in the world, with experts citing healthy diet, high quality health care and a tradition of active pensioners as factors in the phenomenon.
The survey was issued ahead of Respect for the Aged day, a national holiday, on Sept. 21.
