South Korea said on Wednesday it would lodge a formal protest to Japan against its decision to ban South Korean vessels from fishing in Japanese territorial waters.
On Tuesday, Japan notified South Korea that it would bar South Korean fishing boats from its Exclusive Economic Zone in northern Japan in retaliation against a fishing agreement signed between South Korea and Russia last year.
Under the agreement, Russia allowed 26 South Korean vessels to fish in the waters around the Kuril Islands.
The islands, known in Japan as the Northern Territories, were seized by Moscow at the end of World War II, and the dispute over ownership is a diplomatic sore point between Russia and Japan.
"We will call in the Japanese ambassador soon to formally protest this decision," a Foreign Ministry spokeman said.
South Korea said Japan's position was that the Korean fishing vessels operating in the Northern Territories had violated Japanese law and the Korea-Japan Fishery Pact.
South Korea said its fishing agreement with Russia had no political significance and was in accordance with standard international practice.
"It has nothing to do with territorial matters. When we made that agreement with Russia, we made sure that it was a matter of fishing only and that there was no political or diplomatic meaning in it," the ministry spokesman said.
"It is international practice to get permission from the country that has effective control over the waters," he said.