Some 40 demonstrators, carrying Japanese "Rising Sun" flags, gathered outside a building where the Tokyo bureau of the Joongang Ilbo daily is located.
Last week an editorial in the daily's Korean and English versions said the 1945 nuclear bombs dropped by US planes, which together killed more than 200,000 people, were justified.
"The Joongang Ilbo, Shame on you!" the right-wingers yelled in chorus. "We will never forgive your anti-Japanese remarks. Go back to the Korean peninsula!"
During the rally the right-wingers also backed outspoken Osaka mayor Toru Hashimoto, who drew fire by saying that women forced to provide sex to Japanese troops during World War II were a military necessity.
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Opinion polls show that a large majority of Japanese disagree with the mayor's remarks on the so-called "comfort women".
Up to 200,000 women from Korea, China, the Philippines and elsewhere were forcibly drafted into brothels catering to the Japanese military during WWII, historians say.
He later pledged to apologise for his comments, while insisting Japan's soldiers were not unique in brutalising women.
Earlier in the day, some 100 right-wingers staged a separate rally in Tokyo against foreign criminals in the country.
"Foreigners who commit crimes must not come to Japan!" the activists yelled as they marched through the capital's entertainment district of Shinjuku.