According to statistics from Japan's Ministry of Internal Affairs and Communications, the number of children aged under 15 dropped to 15.71 million as of April 1, the lowest level since data became available in 1950.
The ratio of children aged under 15 to the overall population also dropped to a record-low of 12.4 percent, down for the 43rd straight year, government data showed.
Regionally, among Japan's 47 prefectures, only Tokyo had more children as of Oct. 1, 2016 than a year earlier, while other prefectures all suffered a decline in the number of children aged under 15.
Okinawa had the highest ratio of children to the overall population, which stood at 17.2 percent, while Akita had the lowest ratio of 10.3 percent.
Japan has been suffering from a trend of population decrease for decades, with its birthrate in 2016 falling to the lowest level since World War II with only 981,000 births.
Earlier government estimates showed that population of Japan could fall to 88.1 million by 2065, almost one third less than the 127.1 million in 2015.