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South Korea has dispatched about 20 gunboats to the disputed waters, and has told Japan to stay away.
In Seoul, riot police guarded the Japanese Embassy as a group of former special forces commandos burned a Japanese flag and denounced Japan's survey plan.
"Japan has again caught the disease of aggression," one placard said.
The disputed waters surround rocky outcroppings _ called Dokdo by Koreans and Takeshima in Japan _ that lie halfway between the countries and are claimed by both. The area, a rich fishing ground, is also believed to have methane hydrate deposits, a potential source of natural gas.
The showdown highlights the rising stakes of rival territorial claims in East Asia, and South Korea's deep-rooted bitterness over Japan's 1910-45 colonial rule.
South Korea has accepted Yachi's trip to Seoul on the condition that Japan suspend its maritime research plan, and Japan was planning to put the survey on hold, Yonhap and Kyodo reported, citing officials from both countries.
At the same time, Japan warned it would consider any interference with its ships a breach of international law.
"We are speaking about survey boats belonging to the Japanese government," Foreign Minister Taro Aso told a parliamentary foreign policy committee Friday. "Any action against them would clearly violate the principles of international law."
Japan maintains the survey is needed to match a South Korean effort to fully map the sea floor and propose its own names for underwater formations such as basins and ridges.
Seoul has long opposed the international acceptance of the name Sea of Japan for the body of water between the two countries, considering it a colonial vestige. Seoul prefers the name East Sea.
Aso said there would be "no need for us to conduct a survey" if South Korea drops it name-change proposal, which would be submitted in June at an international sea-mapping conference in Germany.
South Korea's Foreign Ministry rejected such a compromise.
"Basically, our position is that we will submit names," said Foreign Ministry spokesman Choo Kyu-ho. "We believe that it is our just right, to register names and make efforts for new names through registration."
The South Korean patrol vessels dispatched to the area are conducting exercises _ but not seizure drills _ in the waters near the island, said South Korean Coast Guard official Jang Soo-pyo.
Park Geun-hye, chairwoman of South Korea's main opposition Grand National Party, urged her government to take a "hard-line" response," saying the territorial dispute was a matter of sovereignty.
"I think there should be no concession on this issue because we have to safeguard our territory no matter what," she said.
The two countries are also at odds over Japanese Prime Minister Junichiro Koizumi's repeated visits to a war shrine that critics, including Seoul, consider a glorification of Japan's imperialist past.