The Health and Welfare ministry estimates that 40% of the population will be of retirement age by 2060.
It says that life expectancy - already one of the highest in the world - will continue to rise.
Correspondents say the report presents a grim picture for Japan at a time when it urgently needs to overhaul its social security and tax systems.
Prime Minister Yoshihiko Noda has pledged to push through a reform programme this year.
But his political opponents say his plan requires higher taxes than are currently proposed.
The government report says that by 2060, Japan will have 87 million people, down from today's 128 million.
The proportion aged 65 or older is expected to double to 40%.
At the same time the national workforce - comprising people aged between 15 to 65 - will shrink to about half of the total population, estimates released by the National Institute of Population and Social Security Research say.
The research says that Japan's population will keep declining by one million people every year in coming decades.
The research also suggests that the average life expectancy will have risen by more than four years by 2060 to 84.19 for men and 90.93 for women.
The population estimate is compiled about once every five years and is based on demographic data used by the government when formulating its social security policy.
The Japanese population is expected to shrink by one third in the next half century, a government report says.