The study by the National Institute of Population and Social Security Research said the population decline will affect all of Japan's 47 prefectures, Kyodo News reported.
The study, also highlighting the country's aging population, said people 65 years or older will account for 30 percent of the total population in 2040. The agency is an affiliate of Japan's Ministry of Health, Labor and Welfare.
The study said it will be the first time all of Japan's prefectures would experience falling population. Of the 47 prefectures, Okinawa in southwestern Japan was forecast to have the lowest decline of 1.7 percent, followed by Tokyo's 6.5 percent.
The study said 25 of the prefectures likely would see a fall of more than 20 percent in their population. Japan's northernmost prefectures of Akita and Aomori were expected to see a decline of more than 30 percent.
Falling fertility rate is one of the factors blamed for the population decline.
In January, the Health Ministry said Japan's population last year was estimated at 125.95 million. The number of newborn babies in 2012 fell to a record low of 1,033,000, down by 18,000 from 2011, and a ministry official had said the pace of decline would only increase as the number of the younger generation decreased.