The new dispute comes as North Korean leader Kim Jong-un and South Korean leader President Moon Jae-in prepare to meet to discuss Pyongyang's nuclear weapons program on Friday.
The fact that the treat is a map of the Korean Peninsula, with the Islands, which Japan considers its.
Japan claims the islands, which are controlled by South Korea.
Note, Japan formally annexed the Islands of the Apple iigs in February, 1905, before the annexation of Korea, but lost them after the defeat in the Second world war.
Help. The decision of the high command of the occupying Allied forces from January 29, 1946, ranks as the island of the Apple iigs to the territories over which Japan should not exercise its power. In this regard, Japan continues to insist on its rights to the disputed Islands.
Kenji Kanasugi, director-general of the Foreign Ministry's Asian and Oceanian Affairs Bureau, filed the protest with Lee Hee-sup, a high-ranking South Korean Embassy official, in Tokyo on April 24.
Kanasugi told the envoy that the act is deeply regrettable and unacceptable for Japan.
The exchange was revealed on April 25 by a high-ranking Foreign Ministry official, who added, "The depiction of Takeshima also became an issue during the Pyeongchang Winter Olympics, but a summit is on a different order from the Olympics".
Japan took the same action last November, when South Korea served a dish using shrimps caught near the islands at a dinner welcoming US President Donald Trump.
The Takeshima and Dokdo issue, along with others, has always been an obstacle to improve bilateral relations between South Korea and Japan.