South Korea has recently sought to revisit the issue of wartime "comfort women" while Japan agreed to apologise to the women and provided a $9.38 million fund to help them under a 2015 deal.
Japan is in no position to declare the issue of wartime "comfort women" settled, South Korean President Moon Jae-in said on Thursday during a speech marking a national holiday commemorating Korean resistance to Japanese occupation.
Japan and South Korea share a bitter history that includes Japan's 1910-45 occupation of the peninsula and the use of comfort women, Japan's euphemism for women - many of them Korean - forced to work in its wartime brothels.
"As the perpetrator, the Japanese government shouldn't say 'it's over'," Moon said. "Wartime crimes against humanity can't be swept under the rug by saying 'it's over'."
But Japan said on Thursday it had lodged a complaint with the South Korean government after Moon's comments.
Japan's Chief Cabinet Secretary Yoshihide Suga described Moon's comments as "extremely regrettable". Suga, speaking at a regular briefing, also urged cooperation between South Korea and Japan to tackle North Korea.
Japan agreed to apologise to former comfort women and provided a $9.38 million fund to help them under a 2015 deal between the two countries. South Korea later said it failed to meet victims' needs and called for more steps.
Meanwhile, South Korea's civil groups and religious leaders hold a memorial for 33 Koreans, who were taken to Japan forcibly during the occupation, and whose remains returned to Seoul on Wednesday to mark the Independence Movement Day.