Environmental group Sea Shepherd condemned the launch of the annual hunt, which follows a recent Antarctic expedition by Japan that netted 680 whales.
"It doesn't matter whether it's 60 or 680 whales, it's too many," said Greenpeace International spokesman Greg McNevin. "They can perfectly well study whales without killing them."
Japan hunts whales using a loophole in a 1986 international moratorium on commercial whaling that allows "lethal research" on the mammals, and makes no secret of the fact that the animals' meat is then served as food.
"The purpose of the research is to collect basic data for resuming sustainable commercial whaling in the future," Hiroko Furukawa, an official at Japan's Fisheries Agency, told AFP on Tuesday.
Four whaling ships and one designated research vessel will set sail from Ayukawa port in northern Miyagi prefecture and hunt whales within 80 kilometres (50 miles) off the coast until late May, the official said.
Greenpeace, which also accuses Japanese whalers of embezzling whale meat, protested last week when Japan's fleet returned from a five-month Antarctic mission.
The mission was marked by tense standoffs at sea with militant activists.
The Japanese Fisheries Agency said the environmentalist group the Sea Shepherd Conservation Society made it impossible for the whaling vessels to operate on 16 days of the 100-day whale hunt.
The six ships caught 679 minke and one fin whale on the mission, the agency said.
That was well below its planned haul of between 765 and 935 of the giant mammals.
Japan will launch the new whaling mission ahead of the International Whaling Commission's annual general meeting in June in Madeira, Portugal.
The focus of negotiations is now whether to allow Japan to conduct commercial whaling near its coast if it scales down the Antarctic hunt.
Japan defends whaling as a tradition and accuses Westerners of disrespecting its culture. It has threatened to leave the IWC if it does not shift to what Tokyo believes is its original purpose, managing a sustainable kill of whales.