The protest came as Seoul and Tokyo are locked in a propaganda war to publicise their respective claims to the islands, known as Dokdo in Korea and Takeshima in Japan.
Google recently updated its Google Maps and on the English-language version replaced the name of Dokdo with Liancourt Rocks, a name taken from a French whaling ship that came close to being wrecked on the islets in 1849.
Google's Korean-language service retains the name of Dokdo, while itsJapanese-language service uses the name of Takeshima.
The South's foreign ministry said Google had notified its embassy in the United States of the name change on October 18.
"At that time, we told Google officials that the name change is unacceptable," foreign ministry spokesman Cho Tai-Young told reporters.
"We made it clear that we can't accept Google's new policy because Dokdo is clearly Korean territory," Cho said. "We will go on with our request to correct it."
In a statement, Google stressed that the name change was not the result of political pressure.
"This update is consistent with our long-standing global policy and was not made in response to any government request," said David Marx, Google's head of Product Communications in the Asia-Pacific region.
"We understand that names of places can raise deep emotions, which is why we have invested so much time to ensure we get to the best outcome for our users," Marx said.
The islands, which lie between the two countries, are controlled by South Korea but claimed by both nations.
The long-standing row over ownership boiled over in August when South Korean President Lee Myung-Bak made a surprise visit to the islets.
Tokyo said the trip, the first ever by a South Korean president, was deliberately provocative.
Lee said it was designed to press Japan to settle lingering colonial-era grievances, including the issue of Korean women forced into sexual slavery for Japanese troops during World War II. Japan colonised Korea from 1910 to 1945.
Japan is also embroiled in a separate row with China over a different set of disputed islands in the East China Sea, which are also claimed by Taiwan.
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