The proceeds from selling whale meat from the hunt are used to fund the research and the data used by the IWC.
However, environmental groups claim it is a pretext to keep whale meat on the market and keep Japan’s whaling industry alive.
Although canned or frozen whale meat is no longer an important part of the Japanese diet it is still easily available at major supermarkets.
Hideki Moronuki, of the Japan’s Fisheries Agency whaling division, said criticism of the programme was unjustified because whaling has become politicised.
"This is a shameless charade"
Ian Campbell, Australian environment minister
"The idea 20 years ago was to temporarily halt commercial whaling because there was a lack of data. Our goal is the sustainable management of whale resources based on scientific data."
Almost half of the IWC members supported the restart of whaling, Moronuki said, but the research programme has many critics.
Ian Campbell, Australia’s environment minister, called on Japan to abandon the project immediately.
"This is not science. These are commercial numbers of whales," he told the Australian Associated Press.
"This is a shameless charade because despite the slaughter of hundreds of whales by Japan, we have yet to see any viable scientific results."
Four protest ships from environmental groups Greenpeace and Sea Shepherd are planning to pursue the fleet to the whaling grounds.