South Korea on Wednesday called for Japan to explain why it had barred entry to a Korean pop star who recently performed on a set of islets claimed by Seoul and Tokyo.

Lee Seung-Chul, 47, was held at Japan's Haneda Airport for hours on Sunday before eventually being sent back to Seoul.

According to Lee, a Tokyo immigration official initially told him the ban was related to a "recent event" reported in the media.

"Then I instantly knew it was about Dokdo ... and knew Japan was exacting its revenge," Lee said in a Monday interview with JTBC TV station.

Lee made headlines in August when he staged a performance -- along with a choir of North Korean defectors -- on the Dokdo islets in the East Sea.

The barren islets are controlled by Seoul, but also claimed by Japan, where they are known as Takeshima.

Lee's performance was timed to coincide with the August 15 anniversary of the Korean peninsula's independence from the 1910-45 Japanese colonial rule.

South Korea's vice foreign minister Cho Tae-Yong told legislators Wednesday that a formal protest would be lodged over Japan's decision to stop Lee entering the country.

"We will summon an official from the Japanese Embassy to demand an explanation," Cho said.

Japan's chief cabinet secretary Yoshihide Suga insisted the entry ban had "nothing to do" with Lee's performance on the disputed islets.

"He was not able to enter Japan because his case met one of the conditions for entry refusal stipulated in our immigration law," he said, without elaborating.

Lee said the immigration official at Haneda Airport had later suggested that the singer's past marijuana use was the problem.

Lee was jailed twice in the 1990s for smoking marijuana, but the singer noted that he had travelled freely to Japan around a dozen times since then.

The row over the islets is just one of a set of historical disputes that have dogged Japan-South Korea ties over the years. (AFP)