Japan has asked South Korea to stop work on a maritime survey in waters around a group of disputed islands.
The islands are small, but highly symbolic in S Korea-Japan relations
The Japanese foreign ministry called the survey "extremely regrettable", and said it had lodged a complaint with the South Korean ambassador in Tokyo.
A ship carrying the Korean research team entered an area Japan considers its exclusive zone early on Wednesday.
Japanese spokesman Shotaro Yachi said that because of the developments, Japan was now considering its own survey.
Last month the two countries narrowly avoided coming to blows after Japan sent boats to investigate the area.
The islands, which are called Dokdo in South Korea and Takeshima in Japan, sit in rich fishing grounds which may also contain extensive deposits of gas.
The islands are currently under South Korean control, and Seoul maintains a police presence there.
The South Korean survey ship entered disputed waters at about 6:40 am (2140 GMT), Japan's coast guard said.
It was soon intercepted by a Japanese patrol boat, and is being monitored through the day, the coast guard added.
Known as Dokdo (Solitary islands) in Korea, Takeshima (Bamboo islands) in Japan
Also known as Liancourt rocks
Japan's and South Korea's claims go back centuries, but islands occupied by S Korea since 1953
Just 230,000 sq m in size, with no fresh water
But surrounding waters valuable for their fishing
In Tokyo, Japanese Vice Foreign Minister Shotaro Yachi summoned South Korean Ambassador Ra Jong-yil to register a complaint about the survey.
But Mr Ra insisted that Seoul had a right to carry out the research, according to Japan's Kyodo news agency.
The dispute has escalated at a difficult time for the two countries, who need to work together to formulate a response to North Korea's recent missile launches.
The tiny islands are about midway between Japan and South Korea.
Tensions over them are fuelled by lingering historical acrimony.
Both countries have centuries-old claims to the islands, which were annexed by Japan in 1905, five years before it annexed the Korean mainland.
After World War II, South Korean coastguards took control of the islands in 1953.
South Korea accuses Japan of failing to repent for its colonial conduct, and the rivalry between the two nations repeatedly flares into confrontation.
The last such argument happened in April, when Japan announced it would carry out a survey of the area.
Tokyo shelved the idea after loud protests from South Korea.