The investigation found officials handling the issue tried to rush to have the deal signed before the end of June under an agreement with Tokyo, and the two countries agreed to make a public announcement on the intelligence-sharing deal only after the signing, Yonhap reported.
The controversy over the pact prompted South Korea to put off signing it last week. And President Lee Myung-bak's office has accepted the resignation of Kim Tae-hyo, who has been criticized over the handling of the deal with Japan, which had been Korea's brutal colonial ruler from 1910 to 1945, presidential spokesman Park Jeong-ha said.
"It has been confirmed that there were procedural problems," Park said. He said officials should have tried harder to "ensure procedural transparency, seek people's understanding and try to persuade the National Assembly, given the unique nature of Korea-Japan relations."
Yonhap noted the public and Parliament were told about the deal only the day before it was supposed to be signed.
Before reaching the cabinet, the agreement was to have undergone a review at a vice ministerial meeting but delays in Japan's consent to the wording of the deal and an internal legal review led officials to skip the vice ministerial session, Yonhap said.
Officials opted to handle the agreement as an "impromptu item" at the cabinet meeting to keep it confidential.
Notable deaths of 2014 [PHOTOS]