For more than five years Nikkyoso members had opposed raising the Rising Sun flag, and singing the anthem, because of their association with pre-war ultranationalism and imperialism.
Nikkyoso has also agreed to accept the ministry's official teaching guidelines which they had been opposing on the grounds that they forced teachers to provide a conservative view of major issues.
Opposition to the ministry of education's decrees had led to the union's members being disciplined and dismissed from their posts. Nikkyoso members have also been excluded from the advisory panels which play an important role in developing ministry policies.
What has been described as the unconditional surrender of Nikkyoso comes after a long period of slumping union membership. The percentage of Japanese teachers in the union has fallen from 80 in 1965 to 34 today.
Eiichi Yokoyama, Nikkyoso chairman, believes its confrontation with the ministry has made the union unpopular with new teachers. "Nikkyoso is adapting itself to a new era," he said at the union's recent annual conference.