Japan's claim to the islands, controlled by South Korea and known in Korean as Dokdo, is set to be included in government-issued teaching guidelines for schools. The manual will also state Japan's position that Russia's South Kuril Islands are "illegally occupied".
South Korea's Yonhap news agency quoted President Lee Myung-bak as saying: "I am forced to express deep regret and disappointment at the Japanese government's decision to define Dokdo as part of its territory in a teachers' manual, particularly in view of the bilateral summit agreement to pursue future-oriented partnership."
The president, who has sought to improve ties with Japan since taking office in February, said his government would deal with the Japanese claim "sternly and strictly."
The Korean Foreign Ministry said Ambassador Kwon Chul-Hyun has submitted a note of protest to the Japanese Foreign Ministry.
South Korea has also sent an extra patrol vessel to the islands in the Sea of Japan, which it calls the East Sea, to bolster its Coast Guard contingent that has been based there since 1954.
Japan claimed sovereignty over the islands, which it calls Takeshima, in 1905, soon before its occupation of Korea, and ceded de facto control after WWII. The islands cover a territory of only 187,000 square meters but are surrounded by rich fishing waters.
While South Korea says it has owned the territory since the sixth century, Japan claims that it had effective control since the 17th century, using the islands as docking points for fishermen.
Yonhap said the Japanese teachers' handbook, to be issued by the Education Ministry and used from 2012, "puts the Dokdo issue on par with Japan's long-running dispute with Russia over the sovereignty of four islands currently under Moscow's control."
Japan's dispute with Russia over the Kuril Islands, annexed by the Soviet Union after WWII, has prevented the countries from signing a formal peace treaty.
At last week's Group of Eight summit in Japan, Russian President Dmitry Medvedev and Japanese Prime Minister Yasuo Fukuda failed to make progress in discussions on the Kurils.