Seoul launched the study on Monday. The survey area will include waters that are claimed by both Japan and South Korea as their exclusive economic zones, and Tokyo loudly protested the move.
Reflecting the tensions over the survey, South Korean officials refused to provide details of the boat's operations or whereabouts.
He said it was unclear whether the ship 'Haeyang 2000,' carrying 33 crew members, entered waters surrounding a pair of islets that are held by Seoul but claimed by Tokyo. The survey will continue until July 17.
South Korea's Maritime Affairs Ministry also said Tuesday it was pushing to set up a division that would handle maritime territory issues, such as naming of waters between South Korea and Japan, the designation of an exclusive economic zone and the naming of underwater physical features in the area.
The waters between the two countries are widely known as the Sea of Japan, but South Korea objects to that name and it should be called the East Sea.
On Monday, Japanese Prime Minister Junichiro Koizumi protested the survey and urged South Korea to use "self-restraint." A Foreign Ministry official said Tokyo could retaliate with its own survey, and the coast guard said it was patrolling to ward off any intrusions into Japanese waters, according to the AP.
Japan and South Korea have long sparred over ownership of the islets, called Dokdo in Korean and Takeshima in Japanese, as part of a wider struggle to define their respective exclusive economic zones.