The group said the Nisshin Maru was spotted trying to cover up a dead minke whale carcass with a tarp when a helicopter approached the vessel in the waters of the Australian Whale Sanctuary.
Captain Adam Meyerson of the Ocean Warrior, Sea Shepherd's newest Southern Ocean patrol ship, says that the crew was caught "red-handed."
Japan's Whaling affairs division of its Fishery Agency said it was aware of the Sea Shepherd statement and photographs, but said it would hold off on commenting until it gets a report of its own from the Japanese vessel.
Sea Shepherd says the photographs it released are the first documenting the killing of whales by Japanese whaling fleets since the International Court of Justice ruled against the program in 2014.
After the ruling, Japan announced new research program, under which it would kill up to 333 Antarctic minke whales each year. The country's Ministry of Fisheries says the program is necessary to study the best methods of managing minke populations.
Australia, New Zealand anti-whaling groups say Japan's exploiting a loophole in the 1986 international ban on commercial whaling, which allows whales to be killed if it's for scientific research.
Australia 'deeply disappointed'
In a statement Monday, Australia's Minister for the Environment and Energy Josh Frydenberg reiterated the country's opposition to killing whales.
"The Australian Government is deeply disappointed that Japan has decided to return to the Southern Ocean this summer to undertake so-called 'scientific' whaling," the statement said.
"Australia is opposed to all forms of commercial and so-called 'scientific' whaling. It is not necessary to kill whales in order to study them."
The Australian Whale Sanctuary
covers Australia's Exclusive Economic Zone, which extends around 200 nautical miles (around 370 kilometers) from the coast.
It's illegal to kill, injure or interfere with whales, dolphins and porpoises within the sanctuary.