Although the number of school-age children has fallen rapidly over the past few years the ministry's latest survey shows that truanting at elementary and junior high schools increased by 13,000 days - 15.5 per cent - from the previous year. This registers the largest increase since the ministry of education, Monbusho, started the survey in 1991.
The sharp rise in truancy has been attributed to problems with bullying and difficulties at home. Also blamed are the rapid changes - such as the increased divorce rate - which a once rigidly conservative society is now undergoing.
The upheaval, say commentators, is beginning to take its toll on Japan's children. The east coast area of Kobe, for example, has been hit by two tragedies in the past few years.
It suffered a massive earthquake in 1995 and a local schoolboy beheaded his 11-year-old playmate earlier this year.
Both events were met by demands from teachers for counsellors to come into schools. Counselling has been rare in Japan, as any form of mental therapy is mistrusted by most people, but attitudes are changing slowly.
The move to introduce counsellors into state schools is thought to have been inspired by the success of such work in the United States, particularly in California.
Launched in 1995, Japan's counsellor scheme uses specialists such as clinical psychologists and psychiatrists. They visit schools twice a week to talk to and advise students, teachers and parents.
Since the start of the scheme there has been a steady increase in the number of requests for counsellors, but, as in Britain, the scheme has been restricted by the ministry's budget.
To increase the availability of counsellors, Monbusho says it is seeking an extra three billion yen (#163;15 million).
Concern for the mental and physical welfare of pupils in Japan, where an alarmingly high number of children commit suicide because of school-related problems, has led Japan's largest teaching union to ask members to turn a blind eye to pupils with problems who played truant.
The Japan Teachers' Union put out a "non-legal" statement at its last conference saying that children were entitled to skip school if this helped to prevent further suicides and to alleviate the misery of victims of bullying who feel compelled to attend school.
Compulsory education is a legal requirement in Japan for children between four and 16 and any non-attendance would seriously jeopardise a pupil's chances of attending high school. Nearly every Japanese child is expected to attend high school.