The ships, led by the 8,030-ton Nisshin Maru, will embark on their largest scientific whale hunt in the South Pacific. Besides humpbacks, they will take up to 935 Antarctic minke whales and up to 50 fin whales.
But it is Tokyo's plans to hunt the humpback, a favorite among whale watchers, that has triggered condemnation from environmentalists.
"These whales don't have to die," said Junichi Sato, a Greenpeace spokesman. "Humpbacks are very sensitive and live in close-knit pods. So even one death can be extremely damaging."
Humpback whales were hunted to near-extinction four decades ago.
But they have been off-limits to hunting since 1963 except for a small number caught under a subsistence whaling program by Greenland and the Caribbean nation of Saint Vincent and the Grenadines. Last year, they caught one humpback each, according to the International Whaling Commission.
The former Soviet Union also hunted humpbacks until 1973 in defiance of the ban, though it is unclear how many were killed.
The American Cetacean Society estimates the global humpback population at 30,000 to 40,000, about a third of levels seen before modern whaling. The species is listed as "vulnerable" by the World Conservation Union.
But Japanese fisheries officials insist both humpback and fin populations, estimated at up to 60,000, are back to sustainable levels.
"Humpback whales in our research area are rapidly recovering," said Hideki Moronuki, whaling chief at the Fisheries Agency.
"Taking 50 humpbacks from a population of tens of thousands will have no significant impact whatsoever."
Moronuki says killing whales allows marine biologists to study their internal organs. Ovaries provide vital clues to reproductive systems, earwax indicates age, and stomach contents reveal eating habits, he said.
Japan also argues that whaling is a Japanese tradition dating to the early 1600s, and has pushed unsuccessfully at the International Whaling Commission to reverse the 1986 moratorium on commercial whaling.
Environmentalists criticize Japan's research program as a pretext for keeping the whaling industry alive, and have long campaigned for an end to the winter catch in the Southern Ocean and a mission in the North Pacific that kills about 100 minke whales a year.