Japan's whaling fleet has returned from the Southern Ocean for another year with its catch of 333 minke whales on board.

Three of the five vessels in the fleet were welcomed on Friday by the mayor and about 200 local people, including the family members of the crew, at the port of Shimonoseki in western Japan.

Japan was able to conduct this season's whaling program under a loophole in the International Whaling Commission (IWC) rules, which allows for scientific whaling.

From now on that loophole will tighten a little: Japan will have to submit its proposed catch to a scientific working group within the IWC.

The commission will ask for further justification about why the scientific program needs to kill the whales to study them.

The Fisheries Ministry said its research was focused on the reproductive and nutritional cycles of minke whales.

"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.

In 2014, in a case brought by Australia, the International Court of Justice found that permits issued by Japan were "not for purposes of scientific research" and instructed the country to halt its JARPA II program.

Japan called off its 2014 hunting season, but submitted a new document to the IWC in the lead-up to the 2015-2016 whale hunt.

The document, titled NEWREP-A (New Scientific Whale Research Program in the Antarctic Ocean), set out its planned catch of 4,000 minke whales over 12 years — that's where the 333 quota per year comes from.

Kitty Block, vice-president of Humane Society International, said it was time whaling of any kind was cast to the annals of history.

"Each year that Japan persists with its discredited scientific whaling is another year where these wonderful animals are needlessly sacrificed," she said.

"It is an obscene cruelty in the name of science that must end."