The demonstrators, members of Chongryon, an organization of ethnic Koreans resident in Japan, carried North Korean flags and portraits of the communist state's leader, Kim Jong Il.
The protests came a day after Japan's Cabinet approved the extension of economic sanctions against North Korea for another six months over the lack of progress in the issue of the abduction of Japanese nationals.
Tokyo demands the return of its citizens abducted in the 1970s-80s. Pyongyang has acknowledged that it kidnapped 13 Japanese citizens, and that it subsequently sent five of them home, but insists that the rest are dead.
The sanctions, originally imposed in October 2006 in response to North Korea's first nuclear test, have already been extended once, in April 2007. They include a ban on port calls by North Korean ships and on all North Korean imports. North Korean nationals are also barred from entering Japan, and Tokyo has halted the export of 24 items, including luxury goods, to the reclusive Communist state.