Sarah Lucas, head of "Australia for Dolphins," filed a lawsuit at the regional court of Wakayama in western Japan on Tuesday, demanding an end to "discrimination based on race" and about seven million yen ($A74,655) in damages.
The activist said on Thursday that she visited the museum in the town of Taiji in February to check on an extremely rare albino dolphin calf, named Angel by her group, which was being kept in a "cramped, abusive show tank".
But a ticket officer turned her away with a sign in English that read: "Please note that anti-whalers are not allowed to enter the museum".
Lucas added she knew other foreigners who had been given the same treatment.
"The museum has not allowed law-abiding people, who wished to see Angel, to enter and turned some people away purely on their appearance," she said, calling the act a violation of the Japanese constitution which bans discrimination based on race.
But the museum's director, Katsuki Hayashi, told AFP that the museum have no intention to discriminate against anyone with the sign.
"We aim to protect the town's culture, assets and fishery," he said. "We welcome (foreigners) who are clearly tourists".
The town has depended on coastal whaling for four centuries, and local fishermen also corral hundreds of dolphins into a secluded bay to kill them for meat or sell them to aquariums and dolphinariums.
Defenders of the hunt say it is a tradition and point out that the animals it targets are not endangered, a position echoed by the Japanese government.