The dispute concerns the Korean-controlled islands that lie between the two countries, which Japan also claims. South Korea refers to them as Dokdo, while Japan calls them Takeshima.
The Japanese government go to the international court by the end of this month, sources told Kyodo.
The court, however, may not hear the case as South Korea was not expected to respond to the Japanese action, but Kyodo said Japan is hoping its unilateral step would at least give publicity to its claim.
Japan has a similar territorial dispute with China over a group of islands in the East China Sea, which has worsened since Japan nationalized the islands last month.
The Japan-Korea dispute is also causing strains in bilateral relations, especially after South Korean President Lee Myung Bak visited one of the islets last August, which drew strong Japanese protest.
Lee also reportedly called for an apology from Emperor Akihito for Japan's 1910-1945 colonial rule of the Korean Peninsula.
South Korea has already rejected Japan's proposal to go to the international court for resolution of dispute, saying it was not worth considering.
Separately, Kyodo reported Japan is also reportedly considering whether to continue with an expanded currency swap agreement with South Korea which expires at the end of this month.
The report also said Japan has not received any request from South Korea to extend the Oct. 31 deadline.
Under the agreement a year ago, the two countries agreed to expand the swap arrangement to $70 billion from $13 billion for one year. The swap deal allows South Korea to exchange its currency for yen or U.S. dollars during market volatility.
With growing bilateral tensions, South Korea's Yonhap News Agency, quoting industry sources, reported Thursday the number of Japanese tourists visiting South Korea has been declining since August after rising in the first eight months of this year.