There were an estimated 16.33 million children aged under 15 as of April 1, down 160,000 from a year earlier, the Internal Affairs and Communications Ministry said.
It was the 33rd straight annual decline and the lowest level since records began in 1950, according to the ministry.
Children accounted for 12.8 percent of the population, the ministry said. In contrast, the ratio of people aged 65 or older was at a record high of 25.6 percent.
Of major countries with a population of at least 40 million, Japan had the lowest ratio of children to the total population -- compared with 19.5 percent for the United States and 16.4 percent for China, Jiji Press said.
Last month, the government said the number of people in the world's third largest economy dropped by 0.17 percent to 127,298,000 as of October 1, 2013. This figure includes long-staying foreigners.
The proportion of people aged 65 or over is forecast to reach nearly 40 percent of Japan's population in 2060, the government has warned.