A Japanese boy born in 2013 can now expect to live 80.21 years, up from 79.94 years in 2012, the health ministry said.
The average lifespan of Japanese women rose to 86.61 years in 2013, up from 86.41 the previous year, making them the world's longest-lived females for the second year running.
In second place were women in Hong Kong, whose life expectancy hit 86.57 last year.
"There is still a room for growth in the lifespan if medical technology advances," a health ministry official said.
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However, Japan's ageing population is a headache for policymakers who are faced with trying to ensure an ever-dwindling pool of workers can pay for the growing number of pensioners.
Government data released in April showed Japan's population shrank for the third year running, with the elderly making up a quarter of the total for the first time.