While China and South Korea have vociferously criticized conservative Prime Minister Shinzo Abe on history, Lee said Singapore approached the issue as a partner of the Japan "which wishes it well."
"Unless you can put the Second World War behind you and not keep on reopening issues of comfort women, of aggression, of whether or not bad things were done during the war, I think that this is going to be a continuing sore," Lee said at the Council on Foreign Relations on a visit to Washington.
Abe has said he will not change a landmark 1993 apology to "comfort women" forced into sex during World War II. But his government last week released a review that said there was no evidence to corroborate the testimony of Korean women in Japanese military brothels.
South Korea responded angrily and summoned Japan's ambassador.
Around 200,000 women -- mainly from Korea but also from China, Taiwan, Indonesia, the Philippines and elsewhere -- were forced to work in brothels for Japanese troops as they stomped around Asia before and during World War II.
While mainstream Japanese opinion holds that the wartime government was culpable, a small but vocal tranche of the political right -- including Abe -- continues to cast doubt, saying the brothels were staffed by professional prostitutes.
Japan captured Singapore in February 1942 in the British military's biggest ever surrender. Singaporean historians say Japanese forces killed 50,000 ethnic Chinese in the island city before surrendering in 1945.
Despite the dark past, Japan had developed warm relations with Singapore and other Southeast Asian nations. (AFP)
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