Japan warned the issue of its wartime system of sex slavery was not a "diplomatic" subject, after US President Barack Obama on Friday called it a "terrible" violation of human rights.
Katsunobu Kato, deputy chief cabinet secretary, said Japan was aware of the suffering of the victims and was trying to avoid politicising the emotional issue.
"Prime Minister Shinzo Abe has said he is deeply pained to think of the people who experienced immeasurable pain and suffering," Kato said in a television programme late on Friday.
"This issue should not be made into a political or diplomatic subject."
In South Korea on Friday, Obama called for an accounting of the wrongs perpetrated by Japanese troops before and during the second world war when thousands of women were forced into prostitution, many from the Korean peninsula.
"This was a terrible, egregious violation of human rights. Those women were violated in ways that, even in the midst of war, were shocking," he said.
But the US president also pressed Tokyo and Seoul to look to the future. Japanese media said Obama was trying to urge both Tokyo and Seoul to stabilise their working relationship.
Obama was calling on Japan to take a proactive stance on the comfort women issue, while also pressing Seoul to overcome emotional reaction, the liberal Tokyo Shimbun said in an analysis.
The influential Asahi Shimbun said South Korea might heighten pressure on Tokyo to address the comfort women issue after the Obama remark.
But the daily said a piece of American advice was also directed at South Korea.
"Obama is seen calling on South Korea to become more flexible because … co-operation between Japan and South Korea has not been able to move forward as South Korea strongly remains hung up on past history," the Asahi said.