Last year's devastating tsunami raised doubts about whether the filming could take place in the territory, but delays in production have paved the way for the studio to set up in the Far East.
"We're doing the stage work in Australia," Rothman told MTV. "The location work will be in Japan."
Hugh Jackman will reprise his role of the mutant anti-hero in the sequel. Its storyline is expected to take its cues from Frank Miller and Chris Claremont's 1982 Wolverine miniseries.
Rothman added: "It's set in Japan. A great number of Japanese actors will be in it and it's based on the very famous run of the comics... I can just tell you on behalf of [Jackman], his goal is to make the ultimate, bad ass, berserker rage Wolverine."
The Wolverine, directed by James Mangold, is scheduled to arrive in cinemas on July 26, 2013.
Watch Hugh Jackman discuss The Wolverine below: