Physical activity has been hampered by a lack of green space in many of the country's cities and a highly competitive education system which means extra classes for the majority of children after school.
Many children go straight from school to juku, a cramming school designed to help them pass college entrance exams. Crowded cities leave them less room for outdoor play, and video games and computers are an added distraction, a ministry official said.
The result, according to Tadashi Arai of the education ministry's sports division, is that children are no longer "using their bodies". Mr Arai said that the physical strength of teenagers had improved yearly after the ministry began its surveys in 1964, but that it levelled off in 1975 and started to decline in 1985. Now the ministry is trying to encourage children to exercise more to help head off disease in later life.
Since the 1950s, Japan's youngsters have been steadily gaining weight as well as height, due largely to a change to a more western-style diet. On average, ninth- grade (14-year-old) boys have increased their height from 1m55 in 1960 to 1m67 today. But more worrying for the government is the increase in pupils' average weight from 45kg in 1960 to today's 55kg average for ninth-grader boys, reflecting the growing number of overweight pupils.
The ministry sees some of the weight problem as a result of its own past recommendation of mostly western menus for school dinners. At the end of the Second World War, Japanese food shortages forced the authorities to use American food aid. This introduced the post-war generations to fatty foods like hamburgers and milk, which have remained staples of the school dinners programme ever since.
Not enough of the extra calories being consumed are being used up by physical exercise. From the second to the ninth grade, pupils receive 105 hours of PE a year, and in the past this would have been supplemented by some form of extra-curricular sports activitysuch as judo. However, these after-school sports are now being replaced by several hours at the local juku, which leaves little time, if any, for any kind of outdoor activity.
On an average weekday, third-year junior high school students spend about 7.5 hours at school and 5.8 hours on extra-curricular activities and private lessons, according to an October survey conducted by the JTUC Research Institute for Advancement of Living Standards. Children are compensating for the lost free time by cutting back on sleep, taking only about 7.5 hours of sleep on weekdays and 8.8 hours on weekends. As well as being unfit, the average Japanese pupil now also complains of stress.