An inflammatory Japanese review has concluded there is no corroboration of evidence given by former so-called "comfort women".
But the government said it would not change Japan's 1993 apology over wartime sex slavery despite the finding.
South Korea's foreign ministry expressed "deep regret" at the review results, which it said "distorted facts" and "undermined" the 1993 apology.
Tokyo's response, which observers say is a messy compromise that looks set to satisfy no one, came as South Korea put on a show of force, holding a rare live-fire drill near islets at the centre of its territorial dispute with Tokyo.
The government of conservative Prime Minster Shinzo Abe said earlier this year it would not reverse the apology, known as the Kono statement, which was issued under a liberal government and acknowledged official complicity in the practice for the first time.
The review, launched as an apparent sop to fellow right-wingers, was putatively established to examine how the decision to apologise was reached, and on what facts it was based.
"There is no change in the government's position to uphold" the 1993 apology, Chief Cabinet Secretary Yoshihide Suga said after the review was submitted to parliament.
"There is no change in Japan's position that we feel our hearts aching over those who suffered hardships that are beyond all description."
About 200,000 women, mainly from Korea but also from China, were forced to work in brothels as "comfort women", serving imperial troops before and during the second world war.
While mainstream opinion holds that the wartime government was culpable, a small but vocal tranche of the political right - including Abe - continues to cast doubt, claiming the brothels were staffed by professional prostitutes.
Suga said Tokyo would give details of the probe by a five-member "verifying team" to Seoul soon, adding no diplomatic slight had been intended with the probe.
Japan's right-wingers would like the apology revoked, something Abe was always under huge international pressure to avoid.
But undermining the evidence on which it is based will further anger historical doves and neighbouring countries.
The issue is a volatile one in South Korea, where feelings run high that Japan has never properly made amends despite a 1965 treaty normalising ties that involved a multibillion-dollar settlement in regard to property and claims.
The issue also infuriates China, which regularly castigates Tokyo on its attitude to the past.