On Thursday Japan's foreign minister told diplomats not to fly Korean Air for a month after it carried out a test flight over disputed islands.
The islands, called Tokto in Korean and Takeshima in Japanese, are claimed by both but controlled by South Korea.
On Friday South Korea's foreign ministry summoned a Japanese diplomat over the boycott.
"From the standpoint of bilateral relations, the Japanese decision is very disappointing," the ministry said.
It added: "Unless there are problems in terms of air traffic control, a Korean flag carrier is free to do anything within our own air space."
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