That large clucking sound you are hearing is the sound of breakdowns in Japan's over-regulated education system forcing some very large chickens to come home and roost in the Kasumigaseki premises of Japan's conservative education ministry, MEXT.
We now discover that the ministry, which fusses in detail over school textbooks, anthem singing and flag-raising ceremonies, claims not to have known anything about the blatant flouting of its rigid and detailed curriculum directives to Japan's high schools.
For years many schools have ignored those directives in order to concentrate on teaching only the few subjects usually needed for university entrance exams -- Japanese and English especially. Subjects such as world history, also compulsory under ministry directives but not compulsory in entrance exams, are bypassed because teaching those subjects would cut time available for key entrance-exam subjects.