Peter Bethune, a member of the Sea Shepherd anti-whaling group, had wanted to make a citizen's arrest of the ship's captain for "attempted murder".
He has been detained on the Shonan Maru 2 since boarding it on Monday.
Japan has six whaling vessels in the Antarctic, where whalers and activists regularly clash during the hunt season.
Chief Cabinet Secretary Hirofumi Hirano told a news conference the country was preparing to bring him to Japan to be questioned under Japanese law.
''We would like to decide whether to file criminal charges against him under Japanese law," Japan's Kyodo news agency quoted Mr Hirano as saying.
Mr Bethune is suspected of illegally boarding the Shonan Maru 2 in the early hours of Monday morning by cutting through its protective netting.
He had said he wanted to arrest the ship's captain, Hiroyuki Komiya, for attempted murder, following a crash between the Shonan Maru 2 and Sea Shepherd's Ady Gil speedboat in January.
Sea Shepherd says the Shonan Maru 2 deliberately crashed into the Ady Gil, destroying the hi-tech vessel.
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