The three-ship mission returned home as Tokyo prepares to make its case to resume commercial whaling at a meeting of the International Whaling Commission (IWC) in Brazil next month.
During the latest 98-day mission, the ships caught 43 minke whales and 134 sei whales, the Fisheries Agency said in a statement.
Foreign pressure on Japan to stop whaling has only made conservatives and politicians more resolute about continuing their push to resume commercial whaling.
It is a rare thorny issue in Tokyo's otherwise amiable diplomacy.
"Data that were gathered during this mission will be analysed, along with results from coastal research programmes," the agency said.
The data "will be presented to IWC's scientific committee, and will enhance scientific knowledge for conserving and managing cetacean resources."
The latest mission was part of a 12-year project to study the number, eating patterns, and biology of whales that Japan wants to analyse to support its claim that certain whales are not endangered and could be caught for consumption.
Japan is a signatory to the moratorium on whale hunting, but exploits a loophole which allows whales to be killed in the name of scientific research.
It makes no secret of the fact that meat from the expeditions ends up on dinner tables, despite a significant decline in the popularity of whale meat.
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