Mr Crean is in Japan for trade meetings, and to advance a Free Trade Agreement (FTA).
Australia this week lodged an application in the International Court of Justice, arguing that Japanese whaling was breaching three international conventions.
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In an interview with Japan's The Nikkei newspaper on Friday, Mr Crean was asked whether he thought trade would be effected by the "deteriorating" relations between the countries, due to the legal action.
"Im absolutely convinced it won't," he said.
"And I don't think the national sentiments are deteriorating."
Both governments had a relationship of maturity and wouldn't let the difference of opinion on whaling interrupt that, Mr Crean said.
"People have known for some years now that there are strong and fundamental differences of opinion between the Japanese government and the Australian government on the question of whaling," he said.
Mr Crean will attend the APEC Trade Ministers Meeting in Sapporo, where he will push for progress on the Doha Round negotiations.
Meanwhile, Japan this week got its fifth leader in six years.
Former former finance minister Naoto Kan has succeeded Yukio Hatoyama, who resigned after eight months in the job.
Mr Crean met Mr Kan in January 2008, and says he expressed "very strong support" for the FTA at that time.
