State-run universities were urged on Tuesday to raise the national flag and sing the national anthem at entrance and graduation ceremonies, as well as other events.
Education minister Hakubun Shimomura made the suggestion at a meeting of the presidents of national universities in Tokyo.
Shimomura said hoisting the Hinomaru flag and singing the "Kimigayo" have long been customary at public schools and are widely expected by the public. However, universities have been divided on the issue.
Shimomura added that his request does not impinge on a university's freedom and that it is up to each institution to make an appropriate decision.
Some critics say Japan's anthem amounts to a call to sacrifice oneself for the emperor and celebrates militarism. Numerous battles over the years have seen teachers clash with school administrators over the issue.
In April, Prime Minister Shinzo Abe said in the Diet that public schools and universities are funded by tax money and that raising the national flag and standing to sing the anthem at ceremonies should be done.
Last month, the Tokyo District Court awarded 537 million yen in compensation to 22 former high school teachers who were punished for refusing to sing the "Kimigayo."
The group said the city refused to rehire them under a scheme that extends employment past the retirement age, because they disobeyed orders to stand and sing the anthem at graduation ceremonies.
In 2012, the supreme court ruled that penalising teachers for not standing to sing the anthem was constitutional, but it warned administrators to exercise care in going beyond a reprimand.© Japan Today/AFP