Seoul lodged an official protest Tuesday with Tokyo after the Defense Ministry in its annual white paper described South Korea-controlled islets in the Sea of Japan as Japanese territory.
The Foreign Ministry in Seoul called in a senior diplomat from the Japanese Embassy to deliver the protest.
A ministry spokesman also issued a statement criticizing the description in the document.
"We strongly protest Japan's including a territorial claim again on Dokdo, which is clearly our territory," the statement said, referring to the islets by their Korean name. Japan refers to the rocky outcroppings midway in the sea between the two countries as Takeshima.
South Korea urges Japan to immediately delete the claim from the white paper and to prevent the recurrence of similar cases, the statement said.
It also said South Korea will never tolerate Japan's territorial claim to the islets.
In a similar move, the spokesman for South Korea's Defense Ministry told reporters the ministry will call in a defense attache from the Japanese Embassy to deliver the protest.
"As soon as the contents of the defense white paper are officially confirmed, we will call in a Japanese defense attache and deliver a stern protest," spokesman Wi Yong-sup said.
Wi also said Japan cannot expect to develop exchanges and cooperation in the field of defense with South Korea unless it retracts its territorial claim over the islets.
The white paper was approved at a Cabinet meeting earlier Tuesday.