Two South Korean demonstrators have each cut off a finger in protest against Japan's claim to a disputed cluster of islands.
Other demonstrators burned Japanese flags and scuffled with police.
South Koreans have reacted with fury as Japan has stepped up its claim to the uninhabited rocks, known as Dokdo in Korean and Takeshima in Japanese.
Seoul says it considers sovereignty over the islands more important than good relations with Japan.
South Korea and Japan had planned to celebrate 40 years of diplomatic relations this year. The governments wanted to emphasise their strong economic links and warming cultural ties.
But the goodwill has been swept aside in a furious Korean reaction to renewed Japanese claims to the disputed islands.
Protesters outside the Japanese embassy showed the depth of their feelings. An elderly woman sliced off her finger with a pair of garden shears and a middle-aged man followed suit using a meat cleaver.
The Japanese ambassador is currently in Tokyo briefing his government on the mood in Korea.
He helped provoke the outcry by claiming publicly last month that the islands are legally and historically Japanese.
South Korean marine police are stationed on the uninhabited outcrops, which are located midway between the two countries.
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