Some of the comments seem to be suggesting that this is because of some Japanese quirk of requiring extreme uniformity far above what is required in other count

Some of the comments seem to be suggesting that this is because of some Japanese quirk of requiring extreme uniformity far above what is required in other countries but it really isn't; it's essentially just laziness on the part of schools. The real reason for these rules is that (as with schools in many other countries for better or worse) Japanese schools don't want their students, who mostly have black hair, to dye their hair brown or other colors. However, since the vast majority of the students naturally have black hair it's just MUCH easier to write the rules to say that in the rare cases where a student has another hair color they have to dye it black rather than trying to argue with students who have dyed "chapatsu" brown hair but then claim that that's really their natural hair color when it isn't. Some schools like high schools in Osaka have a system where students with natural colors other than black are supposed to register so the school can record their natural hair color to know that they aren't dying it. It's pretty dumb and it sucks for the students who naturally have brown hair but it's easy for the school to be lazy and take the approach of just requiring all the students to have black hair.