Shimojo Masao, a Takushoku University professor with very rightist views on territorial issues, arrived at the Incheon International Airport on an Asiana Airlines flight at about 9:30 p.m. on Sunday, according to the police.
But the nationalistic professor was immediately denied entry to the country by immigration officials due to the local justice ministry's disapproval of his visit, they said.
The professor did not clash with officials and boarded a flight back to Japan after an four-hour stay in a waiting room at the Incheon airport, the police said.
Whether Shimojo will try entry to South Korea again is still unknown, but immigration officials said he was not on the list of those seeking to enter the country.
The failed attempt to enter Korea by the Japanese historian, who has repeatedly claimed his country's ownership of Dokdo, came ahead of the planned visit late Monday morning by three lawmakers from Japan's conservative opposition Liberal Democratic Party (LDP).
LDP lawmakers said they will visit Ulleung Island near Dokdo as part of efforts to reassert claims to the volcanic islets that they say are Japan's territory.
South Korean foreign ministry officials, however, have warned the Japanese lawmakers against the planned visit, saying they will not be allowed to enter South Korea to visit Ulleung Island, about 90 kilometers west of Dokdo.
The latest diplomatic tensions over Dokdo started early last month when Japan imposed a one-month ban on the use of Korean Air flights by its diplomats in retaliation for the airline's June 16 test flight of its first Airbus A380 plane over the South Korean islets.
South Korea demanded Japan immediately withdraw the measure, but Tokyo has refused to do so.
Japan's claims to Dokdo have long been a source of diplomatic friction in relations with South Korea as resentment over Japan's 1910-45 colonial rule of Korea still runs deep here.