The country's child population hit the lowest level since comparable data became available in 1950.
The ministry released the data a day before Children's Day.
The number of boys stood at 6.99 million, and that of girls was 6.66 million.
The proportion of children in the country's overall population came to a record low of 11.1 %, dropping for 51 years in a row.
According to UN and other estimates with different survey periods, Japan had the second-lowest share of children in the total population among 37 countries with a population of more than 40 million.
South Korea had the lowest share, at 10.6 %.
The latest ministry data showed that the number of children aged 12-14 stood at 3.14 million in Japan, followed by those aged 9-11, at 3.02 million, those aged 6-8, at 2.78 million, those aged 3-5, at 2.5 million, and those aged zero to 2, at 2.22 million.
According to data as of Oct. 1 last year, all 47 prefectures in Japan logged year-on-year decreases in child population.
Only Tokyo and neighbouring Kanagawa Prefecture had a child population of over one million. Also by prefecture, Okinawa had the highest proportion of children, at 15.8 %, followed by Shiga and Saga, each at 12.7 %.
The lowest share was 8.8 %, in Akita, followed by Aomori, at 9.8 %, and Hokkaido, at 9.9 %.
[Copyright The Jiji Press, Ltd.]
Photo by Reuters