Japan demanded today that South Korea halt a survey of disputed waters between the two nations that started earlier in the day, but Seoul said it had a right to exercise its sovereignty over the area.
Tokyo also said it may resurrect its own survey of the waters, which it called off in April following talks with Seoul.
A South Korean survey ship escorted by a patrol boat entered what Japan considers to be its exclusive economic zone near islands at the centre of a territorial dispute between the two countries at about 10:40 pm (Irish time), Japan's coast guard said.
The islands sit in rich fishing grounds, and South Korea's state gas company says they lie above unexploited gas hydrate deposits potentially worth billions of dollars.
Japanese Vice Foreign Minister Shotaro Yachi summoned South Korean Ambassador Ra Jong-yil to a meeting to lodge a protest against the survey, the foreign ministry said.
Ra told Yachi that Seoul had a right to conduct the survey and the discussion ended without agreement, Japan's top government spokesman Shinzo Abe told a news conference.
Japanese Foreign Minister Taro Aso also protested to his South Korean counterpart, Ban Ki-moon, in a telephone conversation later today, Aso added.
The dispute has escalated just as Japanese officials said they wanted to work closely with neighbouring countries to formulate a response to North Korea's launch of a series of missiles earlier in the day.
South Korea and Japan are both parties to six-way talks on Pyongyang's nuclear programme.