In a separate statement, the foreign ministry threatened unspecified "reciprocal countermeasures" if the revisions are not withdrawn immediately.
The Dokdo islands, known as Takeshima in Japan, are controlled by South Korea but claimed by both countries.
The Japanese education ministry has instructed teachers in junior and senior high schools to use amended manuals stating that the islands belong unequivocally to Japan.
The revisions apply both to the Dokdo/Takeshima dispute and to another set of islands whose sovereignty Japan disputes with China.
"We called in the ambassador to lodge a strong protest ... after the Japanese education ministry maliciously included groundless allegations in textbook teaching manuals," South Korean Vice Foreign Minister Kim Kyou-Hyun told reporters invited to witness the convocation of Ambassador Koro Bessho.
The separate foreign ministry statement accused Japan of "holding on to its past bad habit of distorting history and nostalgia over past imperialism."
Japan's 1910-45 colonial rule over the Korean peninsula remains a hugely emotive issue in South Korea, which feels successive Japanese governments have failed to properly apologise or atone for abuses committed during the period.
The island dispute is seen by most South Koreans as evidence of Japan's continuing bad faith and held up as an argument against Prime Minister Shinzo Abe's desire to revise his country's pacifist constitution.
"We cannot but ask Japan how it could contribute to international peace and stability ... and play a greater role in the international society while it keeps creating conflicts with its neighbors and threatening regional peace and stability," the foreign ministry said.
Relations hit a new low in December when Abe made his first visit since taking office to a controversial war shrine which commemorates around 2.5 million Japanese war dead including several high-level war criminals.
South Korea and China said the visit was a symbol of Japan's failure to repent its 20th century warmongering.
South Korean President Park Geun-Hye has refused to meet with Abe since she took office nearly a year ago.