The two ships will take measurements for a map of the islands that are administered by South Korea but claimed by Japan, renewing a feud tied to colonial history that has undermined relations between the neighbours.
The South Korean coast guard said on Wednesday 18 patrol ships were deployed around the uninhabited islets - called Dokdo in South Korea and Takeshima in Japan - with a surveillance plane ready to scramble.
"Japan must immediately cancel its plan to survey the area. We will take stern measures if Japan pushes ahead with the survey," the foreign minister, Ban Ki-Moon, said after a national security meeting led by the president, Roh Moo-Hyun.
"Japan must take full responsibility in case of any physical clash," said Song Min-Soon, Roh's foreign policy adviser.
South Korea says the area is part of its exclusive economic zone, but Japan says the two countries' zones overlap there.
The Japanese coast guard vessels were set to head on Wednesday to the disputed area from the port of Sakaiminato in southeastern Japan, Nippon Television said. They will return to Tokyo on April 26, Kyodo News said.
"Surveys like this are also conducted by other countries. We should handle this calmly under international law," said Shinzo Abe, the chief cabinet secretary and spokesman for the Japanese government.
South Korea's coast guard has
deployed 18 patrol boats
Japanese coast guard spokesman Yoshiichi Shinde declined to give details of the ships' itinerary, saying Tokyo was "trying to avoid provoking further South Korean excitement".
Tokyo's claim to the islets has angered South Korea. Bitter memories remain of Japan's brutal rule over the Korean peninsula from 1910 to 1945.
Japan said the survey was being carried out because an international oceanographic meeting in June is set to consider a proposal to use Korean names for geographical features on the seabed.
"The aim of this survey is to collect necessary data so that we can submit an alternative proposal," Shotaro Yachi, Japan's vice foreign minister, said on Monday.
North Korea has offered moral support to Seoul, saying Japan has become "ever more shameless" in attempts to distort history and expand its territory.