Moon said that though the deal was an official promise approved by the leaders of both countries, he as a president of South Korea should make it clear again that the comfort women issue can not be resolved by the 2015 deal.
In the statement, read out by a spokesman, President Moon said it has been confirmed that there were problems during the negotiations, regarding the procedures and the content.
"If the South Korean government tries to change an agreement that is already being put into practice based on this report, relations between Japan and South Korea will become unmanageable", Japanese foreign minister Taro Kono said.
Relations had only begun to recover in the two years since an agreement on the South Korean "comfort women", who were forced to work in Japanese brothels during the Second World War.
Instead, Tokyo made a 1 billion yen ($9 million) financial contribution to a victims' trust fund created by the agreement as its reparations mechanism, the report noted, but refused to link the money to any legal responsibility.
While the South Korean presidential office is seeking to decide on a stance on the agreement before the start of the Pyeongchang Olympics in February, the release of the results will likely heighten criticism within South Korea toward the bilateral agreement. He has said several times that the deal is not supported by the South Korean people.
"This runs afoul of the established universal principle of the global community for settling history issues, and above all, it was a political agreement that excludes the victims themselves and citizens", Moon said of the deal.
He expressed his deep consolation for the victims who were scarred once again by the existence of the undisclosed agreements, saying truth is the most important thing in facing history.
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Moon pledged to normalise relations and work towards "future-oriented cooperation" with Japan.
Moon had reviewed the agreement soon after taking office in May and has repeatedly stated that the deal is not supported by the South Korean people.
Among the talks kept in secret, Japan told Seoul to refrain from supporting relevant civic groups disagreeing with the deal and to stop using the phrase "sexual slavery". "The Japanese government strongly requests that the South Korean government reliably and continually implement its "final and irreversible" agreement".
Japan temporarily removed its ambassador to South Korea after activists erected a statue honoring the women outside of the Japanese consulate in South Korea.
The countries resolved to refrain from criticising each other over the issue at worldwide forums, and South Korea agreed to "make efforts" to secure the removal of statues honouring the women, including one outside the Japanese embassy in Seoul.
Although it did not make any policy recommendations, the task force advised the government to come up with long-term solutions in dealing with historical issues.
The report criticized the administration of former President Park Geun-hye for failing to adequately seek the opinions of the victims before reaching the deal.
The foreign minister has previously said the government will take the task force's review into consideration when formulating a new policy, but that it also needs more consultation with the victims and related parties.
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