Japan's whaling vessels returned to port with 333 minke whales on Friday after its months-long Antarctic hunt.
The Fisheries Ministry said the whales were killed in the name of science.
"The purpose of this research is to carry out a detailed calculation of the catch limit of minke whales and study the structure and dynamics of the ecological system in the Antarctic Ocean," it said.
Japan plans to hunt nearly 4,000 whales over the next 12 years despite the International Whaling Commission's 1986 moratorium on commercial hunting. The country launched its "scientific whaling" program in 1987 as a loophole to the moratorium.
Reuters noted that Japan's ultimate goal is the resumption of commercial whaling. Japan insists that most whale species are not endangered and that eating whale is part of its culture, even though most Japanese people no longer eat it.
Conservation groups have rebuked the most recent hunt.
"Today Sea Shepherd mourns the loss of these whales," the marine wildlife conservation organization said. "We have called an emergency meeting of the Global Board of Directors in Amsterdam this weekend to review our whale defense strategy in the Southern Ocean, and will release a more detailed statement on Monday morning."
Sea Shepherd's long-running Operation Nemesis campaign has a mission of ending Japan's whaling program. The group is urging governments to "stop making hollow statements of disapproval and start taking action to hold Japan accountable" or the "needless slaughter of marine life will continue."
Kitty Block, the executive vice president of Humane Society International, had similar sentiments.
"There is no robust scientific case for slaughtering whales," Block said. "Commercial whaling in this, or any other disguise, does not meet any pressing human needs and should be relegated to the annals of history."