A dwindling birth rate is expected to cut Japan's population by 30% over the next 50 years
The report says the current population of about 127m is projected to sink below 90m by 2055.
By that date the proportion of the population aged above 65 is set to double to 40.5%.
Prime Minister Shinzo Abe pledged to bring in policies that would prevent further falls in birth rates.
Correspondents say the current trend is caused by women marrying later in life and having fewer children.
In 2005 for the first time since World War II the Japanese population declined, the survey by the National Institute of Population and Social Security Research for the ministry of health noted.
Japan already has the highest number of elderly people and the lowest number of young as a percentage of its population.
The imbalance is threatening future economic growth and raising fears over whether the government will be able to fund pensions.
But Chief Cabinet Secretary Yasuhisa Shiozaki said: "It's impossible for the pension system to collapse due to the declining birth rate because we will adjust the amount of money put into it."
Mr Abe unveiled a draft budget on Wednesday that seeks to increase support for child-care services.
Japan's population expected to plunge 30 percent by 2055
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