But not everyone agrees, including the United Nations International Court of Justice. In 2014, the court ordered Japan to halt the program after concluding that research claims couldn't justify the number of kills.
Japan temporarily stopped the hunt and proposed a new plan: 4,000 whales killed over 12 years. The International Whaling Commission asked Japan to revise the plan again, but the Asian nation went ahead and resumed the controversial hunt in late 2015.
The fleet spent four months in the Antarctic, killing 333 minke whales, 207 of which were pregnant.
"The number of pregnant females is consistent with previous hunts, indicating that the breeding situation of minke whales in the Antarctic is healthy," the Japanese Fisheries Agency said in a statement, Reuters reported.
The Fisheries Agency said it also conducted non-lethal research. "Attaching GPS devices helps us study minke whales' migration routes by tracking them for several days," agency official Hiroyuki Morita told AFP.
Conservationists say labeling the hunt as scientific is a way to skirt international rules; the International Whale Commission allows for scientific exemptions from its 1986 commercial whaling ban.
Australia strongly condemned the hunt on Friday. Among the most vocal critics of the practice, Australia brought the International Court of Justice case against Japan.
"The Australian government opposes so-called 'scientific' whaling clearly, absolutely and categorically," Australian Environment Minister Greg Hunt told AFP on Friday. "It is in my view abhorrent and a throwback to an earlier age... There is no scientific justification for lethal research."
Hunt has previously said that "nonlethal research techniques are the most effective and efficient method of studying all cetaceans."
Many of the whales end up as meals, as the surplus is sold off. As Speaking of Science has reported previously:
Japanese officials don't hide the fact that the meat from these research animals is butchered and sold commercially. But they argue that minke whales are abundant enough to be hunted sustainably, in any case. Minke whales are indeed the most common baleen whales in the ocean, and they're not endangered. But some conservationists point to a steady decline in the animal's numbers over the course of the past few decades as a warning against even this "sustainable" whaling.
[This post, originally published March 24, has been updated.]