"School lunches with menus that are created by nutritionists are provided to all primary schools and the majority of junior high schools throughout Japan," Mitsuhiko Hara, a pediatrician and professor at Tokyo Kasei Gakuin University, told AFP.
The lunches are mandatory -- no packed lunches allowed -- and while they are not free for most, they are heavily subsidised.
Each meal is designed to have around 600-700 calories balanced between carbohydrates, meat or fish and vegetables.
One sample meal served to children in Japan's Gunma gives a flavor: rice with grilled fish and a spinach and sprout dish, served with miso soup with pork, alongside milk and dry prunes.
"School lunch is designed to provide nutrition that tends to be lacking in meals at home," education ministry official Mayumi Ueda told AFP. "I think it contributes to the nutritional balance necessary for children."
Unlike the cafeteria system operated in some Western countries, Japanese school lunches are usually served in the classroom. Pupils frequently dish out the food to each other and clean up the room afterwards.
The Japanese government studies nutrition and eating habits in Japan annually, and uses the results to shape what goes into the school meals, she added.
School lunches in Japan date back to as early as 1889, when rice balls and grilled fish were provided for children living in poverty in northern Yamagata prefecture.
But the program was expanded nationwide after World War II ended to address childhood hunger amid serious food shortages.
And there are other factors at work, Hara acknowledged.
"Because many Japanese are health-conscious, they try to eat a variety of food, which is good," he said.
"And we're taught to eat seasonal food, which also contributes to good health. Japan is one of the rare countries that pay so much attention to food that is associated with specific seasons," he added.
The results are clear in the statistics: Japan has one of the world's lowest rates of infant mortality, and the rate of children aged five to 19 who are overweight or obese is 14.42 percent, far lower than most other developed countries.
Hara said another factor in Japan is regularly mandated childcare health checks. Parents of infants receive reminders from the local government, and children are given health checks at school, including measuring height and weight.