"The fact that the Japanese crew went to cover up their harpoons and the dead minke whale on deck just shows that they know what they're doing is wrong".
The incident is first to be reported since a 2014 ruling against Japan by the International Court of Justice (ICJ), according to Sea Shepherd.
"The Australian government needs to come clean and do the job that they should be doing, defending the whales in the southern ocean whale sanctuary".
The dead whale has been found a day after Japan's Prime Minister Shinzo Abe had an official state visit to Australia.
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He reiterated figures from a poll in December 2015 that found 80 percent of Australians wanted a customs ship sent to the Southern Ocean to monitor Japan's whaling fleet. Footage shows the dead whale was later covered by a blue tarpaulin.
The Nisshin Maru collided with Greenpeace's MV Arctic Sunrise in 1999 and 2006, with both ships claiming the other rammed them, and it also collided with the Steve Irwin and Bob Barker in 2013.
Japan cancelled its 2014-15 hunt after the ruling, but restarted it the following year under a new programme with a two-thirds cut in the target catch number - saying the fresh plan was genuinely scientific.
"A soon as the whaling fleet saw that Sea Shepherd on the scene, they were scrambling to cover up their illegal operations, they were covering up their harpoons", Mr Hansen said.
Meanwhile the ship Steve Irwin is now on a course to intercept the Japanese whaling vessel, and the group is now not disclosing the location of its other ship Ocean Warrior "for strategic purposes".
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"No country has done more to try to end whaling than Australia". Japan insists that since then it has only been whaling for "scientific research", but the activists doubt that slaughtering more than 8,000 minke whales in the past three decades for that goal was necessary.
'It is not necessary to kill whales in order to study them'.
"We [Sea Shepherd] are the only ones there between the harpoons and the whales", he said.
Australian Greens Senator for Tasmania Nick McKim said that "Japan should not be let off the hook" and the global community need to enforce the jurisdiction of the worldwide Court of Justice.
He said Australia would continue its efforts in the International Whaling Commission to strongly oppose whaling and promote whale conservation.
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