Tokyo Gov. Shintaro Ishihara on Friday defended the Tokyo metropolitan education board's order that all schools display the flag and sing the national anthem at ceremonies.
On Thursday, Emperor Akihito said teachers and students should not be forced to sing the national anthem and pay homage to the flag.
The board has already punished 243 teachers for refusing to stand and sing the contentious "Kimigayo" anthem at school ceremonies or not forcing their students to do likewise.
The nationalist governor told a regular news conference: "It's a matter of whether public servants do or do not comply with it as an obligation the state has decided on. This is different from the general idea of whether something should be forced.
"I don't want the two matters to get mixed up."
Referring to the Emperor's remark, Ishihara said: "I wasn't nearby (at the time), and so (I don't know) the (actual) dialogue and the nuance. I do not want to comment any further."
Many teachers have filed lawsuits against the board.