A government official said on Friday the rejection was a routine decision as the German man said he was in the country for sightseeing but did not have sufficient documentation or plans.
"A 37-year-old man was refused entry because there were significant questions regarding his purpose for entry," the official said, without elaborating further.
Local media named the man as Martin Kraemer, who arrived in the northern island of Hokkaido on Monday aboard a freighter from Russia. He was scheduled to attend an anti-G8 summit rally on Saturday in Hokkaido's largest city of Sapporo, Kyodo News reported.
He failed to show a return ticket to immigration authorities and is still staying on the docked cargo ship, according to the Yomiuri Shimbun.
"I will go anywhere where there is a need to protest against the summit," Kraemer told local reporters, according to the Yomiuri's evening edition. "The purpose of my visit was sightseeing. I want to engage in talks in order to create a better labour environment and better society."
The German government confirmed the events and said it had no objections to
the actions of the Japanese authorities.
"The embassy in Tokyo has been providing consular services to the man in question since March 10," Foreign Ministry spokesman Martin Jaeger told a regular government news conference.
"The man himself refused to leave for a third country and that is why he will be put on a ship in Japan, probably today, to take him back to Russia. We must respect the fact that every country ... has the right according to its own laws to allow entry or not. I assume that the Japanese authorities acted in compliance with the law."
Japan plans to hold the Group of Eight summit from July 7-9 in the northern mountain resort of Toyako, which was chosen partly because of its remote location and is considered ideal for security. It is set to be United States President George W. Bush's last summit of the G8, which also includes Britain, Canada, France, Germany, Italy, Japan and Russia.
Japan last week also refused entry to a South Korean activist who hoped to take part in a pre-summit forum on farmers' rights. The immigration department gave no reason for turning her away but she was allowed in after flying back to South Korea and then returning.