Tokyo's claim to the islands was included in the 2023 Diplomatic Bluebook — Japan's annual report on foreign policy and activities — which was released earlier on Tuesday.
Seoul "strongly protests Japan's repeated unjust claims of sovereignty over Dokdo, which is of our sovereign territory historically, geographically and under international law," Lim said, as quoted by South Korean news agency.
The spokesperson added that Tokyo should "clearly recognize" that such repeated claims do not contribute to the development of ties between the countries.
The foreign ministry also called on Naoki Kumagai, the deputy chief of mission at the Japanese Embassy in Seoul, to deliver a formal protest message, the report said.
The Liancourt Rocks — called Dokdo Islands by Seoul and Takeshima Islands by Tokyo — lie almost equidistant from Japan and South Korea, with the latter maintaining a small police force there. For decades, the islands have been a bone of contention, with both sides claiming they have long-standing historical ties to the archipelago, which is believed to be rich in natural resources.