In an unusual intervention in the discussion, Naruhito's mild-mannered broadside was being interpreted in some circles as a rebuke to Prime Minister Shinzo Abe, a key figure in the right-wing drive to minimise the institutionalised system of wartime sex slavery.
"Today when memories of war are set to fade, I reckon it is important to look back our past with modesty and pass down correctly the miserable experience and the historic path Japan took from the generation who know the war to the generation who don't," Naruhito said.
The prime minister last week appointed a 16-member panel to advise him on a statement he is set to make later this year to mark the 70th anniversary of Japan's surrender.
Abe has said he will largely stand by Tokyo's previous apologies, but amid growing anger in China and South Korea over the "comfort women" system, speculation is mounting that he will seek to downplay the issue.
Mainstream historians agree that up to 200,000 women, predominantly from Korea, were forced into sexual slavery during WWII.
Both countries will be carefully watching any official pronouncement on the war.
While Japan's newspapers remained staid in their coverage of Naruhito's comments, social media users leapt on them.
"This definitely contains a warning against Shinzo Abe, doesn't it?" tweeted @Kirokuro.
"It is a regular recognition (of history), but these comments by the crown prince stand out because Prime Minister Abe's views on the constitution and history are outrageous," said @kazu_w50
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