Sarah Lucas, head of the group "Australia for Dolphins", is seeking seven million yen ($69,000) in damages over claims that include she and her father were "rudely and aggressively escorted" from the Taiji Whale Museum in February.
The regional court in Wakayama prefecture heard that the pair were watching a dolphin show when the alleged incident happened in the town of Taiji, about 450 kilometres (280 miles) south of Tokyo.
The activist had been on her way to check on the condition of an extremely rare albino dolphin calf which had been captured a month earlier.
Lucas said she and her father returned again several days later when a ticket officer showed them a sign with large English letters that read: "No anti-whalers are allowed inside the museum."
"It is unforgivable for them (the museum) to accept only those whose thoughts are likable for them," plaintiff lawyer Takashi Takano told the court, according to a press release issued after the hearing.
"It is against various statutes including the constitution and international covenants on human rights."
The lawsuit claimed that the museum's barring of "foreign-looking visitors" violated Japanese law, which prohibits discrimination based on race or creed.
"I believe the museum had no right to assume, based only on a single glance, that my father and I are troublemakers or bad people," Lucas told the court, the statement said.
The defendants' lawyer declined to comment on the case when contacted by AFP.
However, the museum's director, Katsuki Hayashi, earlier said that "we welcome (foreigners) who are clearly tourists.
"We aim to protect the town's culture, assets and fishery," he added.
Taiji, which garnered international headlines after its appearance in the 2009 documentary The Cove, has become a flashpoint in a fight by activists to stop Japan's whaling programme and the town's dolphin slaughter.
In the annual hunt, local fishermen corral hundreds of dolphins into a secluded bay to kill them for meat or sell them to aquariums.
Defenders of the bloody hunt say it is a tradition and point out that the animals it targets are not endangered, a position echoed by the Japanese government.
They say Western objections are hypocritical and ignore the killing of other animals for food, including cows and pigs.
The next court hearing is set for mid-September.