During the voyage, Australian, French and New Zealand scientists used nonlethal techniques to study whales. It was a challenge to Japan's scientific program, which kills up to 1,000 of the mammals a year - an allowed exception to the International Whaling Commission's 1986 ban on commercial whaling.
Critics say the program is a front for commercial whaling, with the whale meat sold for consumption in Japan.
The expedition that ended Monday was the first in a five-year research program in Antarctica that was proposed by the Australian government and agreed to by the IWC.
The scientists' research focused on whale numbers, what they eat, how they move between food patches and how they travel to and from their breeding grounds in the central Pacific.
"All of those questions can be and are being answered using nonlethal techniques," expedition leader Nick Gales told reporters Monday.
While Gales acknowledged that Japan does some "marvelous" nonlethal whale research, he said "the component of their work that results in the killing of the whales" is not the type of science the IWC requires.
Toshinori Uoya, a Japanese Fisheries Agency official in charge of whaling issues, told The Associated Press in Tokyo there are some data "that we can obtain only through lethal approach," including age, stomach contents and fertility rate.
He said Japan is open to any new nonlethal methods if they are proven effective.
Peter Garrett, Australia's environment minister, said in a statement that the research showed "effective and achievable ways to collect a whole range of important data without the need to kill these mammals."
The scientists counted mainly humpback whales, taking photos and biopsy samples from 60 of them, and attaching satellite tracking devices to about 30 of the animals to study their feeding and travel patterns.
The researchers found fairly strong recovery in some populations of humpback whales, but Gales said blue whale numbers are down around 2 percent from what they once were in Antarctic waters, after being "enormously heavily exploited during the industrial whaling era."
The group saw quite a few Antarctic minke whales along the ice edge, Gales said, but the scientists were unable to study them because of difficult ice and weather conditions.
Minke whales make up the bulk of Japan's annual hunt in Antarctic waters.
Other member countries of the 13-nation Southern Ocean Research Partnership will participate in future trips, Gales said.
Results of the voyage will be reported to the IWC at its annual meeting in Agadir, Morocco, in June.