"Japanese whaling ships have been sighted with their harpoons uncovered in the Southern Ocean, where a moratorium on whaling is now in effect", he said in a statement.
This is the second time the Japanese whaling fleet has returned to the Southern Ocean since an International Court of Justice ruling in 2014 that such activities contravened the rules of the International Whaling Commission.
Sea Shepherd claimed the Nisshin Maru crew "scrambled" to cover the dead whale with a tarpaulin after spotting the anti-whaling group's helicopter.
Jeff Hansen, the managing director of Sea Shepherd Australia, said a "lack of action by the Turnbull government" in response to the killing of whales in Australian waters on the tail of a state visit from Abe showed "the government has no spine when it comes to protecting the wishes of Australians to defend the Southern Ocean whale sanctuary".
The slaughter of at least one protected minke whale - shown in Sea Shepherd pictures lying on board the whaling mother ship, Nisshin Maru - has allegedly taken place in Australian waters in the Southern Ocean.
A whale conservation group published photographs of a Japanese ship with a dead whale on board, the first such images since the International Court of justice found the Antarctic whaling program illegal in 2014.
Australia, which opposes all forms of commercial and scientific whaling, will continue raising its concerns about the issue with Japan, Australian Foreign Minister Julie Bishop told Reuters.
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The two leaders spoke about the proposed Trans-Pacific Partnership and defence issues, but also reportedly discussed whaling.
Dark blue marks the waters of the Australian Whale Sanctuary, with a red circle marking the area where Nisshin Maru was sighted according to Sea Shepherd.
Sea Shepherd maintains that the action was done within the Australian whale sanctuary.
Australian Minister for the Environment and Energy Joshua Anthony referred to the news as "disappointing".
"We know that the fleet is heavily funded by Japan ... it's Shinzo Abe's whaling fleet".
Meanwhile, Environment Minister Josh Frydenberg has released a statement to condemn the resumption of whaling. Japan started what it calls "scientific whaling" in 1987, a year after an worldwide whaling moratorium took effect.
Japan has reportedly hunted more than 8,200 minke whales in the Antarctic since 1986 despite an global freeze on commercial whaling - claiming that it is whaling for "scientific research".