The islands issue has long been a nationalist touchstone in Korea
Advertisements promoting Japanese condoms have been removed from Korean underground trains amid a rekindled territorial dispute.
The action was taken following complaints from passengers, a Seoul Metro spokesman told AFP news agency.
"If the territorial dispute with Japan over Dokdo had not flared up again, such complaints would not have been lodged with us," said Kim Jeong-hwan.
Dokdo is the Korean name for islets known as Takeshima in Japan.
Both Korea and Japan say they have a historical claim to the islands, and the issue has been a persistent irritant in relations.
This week Korea recalled its ambassador to Tokyo after new teachers' guidelines produced in Japan reaffirmed the claim to ownership.
Now it has emerged that about 200 ads for Japanese condoms - bearing the strapline "No. 1 in Japan" - have been taken down from Korean trains.
The islands are small, but have symbolic and economic importance
"There were public complaints about promoting Japanese condoms and we immediately took action," Mr Kim said.
Protesters threw tomatoes and rotten eggs at the Japanese embassy in Seoul on Wednesday.
Meanwhile, a spokesman for Korean President Lee Myung-bak said he was considering further moves on the issue, including possible legal action, reported Korean news website Hankyoreh.
The islets, which are roughly equidistant from Korea and Japan, are small, but lie in rich fishing grounds which could also contain large gas deposits.
But the dispute also taps into lingering grievances over Japanese colonial rule of Korea until 1945.