The fleet, comprising four whalers, will set sail from Ishinomaki in northeastern Japan with a target to hunt a maximum of 51 minke whales in an area of around 80 km, EFE news reported.
The aim of the programme, according to the agency, is to study the contents of the stomach and other scientific facets of the captured whales to better manage their population.
Japan captured 333 rorqual whales between December 2015 and February 2016 under its hunting programme in the Antarctic.
Although the country suspended its operations in the area after the International Court of Justice banned whale hunting in the Antarctica, it resumed them in December after introducing changes in the programme, including a decision to reduce the catch volume.
Japan, which signed a total moratorium on commercial whaling that came into force in 1986, launched scientific capturing programmes the following year.
Japan’s whale hunting programs have been harshly criticised by many countries that consider them as covert commercial fishing, given that the whales captured are later sold for consumption.