The four-month expedition in the Antarctic ended in March after the fleet killed 333 minke whales, according to a report submitted by Japanese authorities to the International Whaling Commission last month.
Of those, 122 were pregnant, according to the Japanese report, with dozens more immature whales among those killed.
Humane Society International, a conservationist group, called the figures “a shocking statistic and sad indictment on the cruelty of Japan’s whale hunt”.
“It is further demonstration, if needed, of the truly gruesome and unnecessary nature of whaling operations, especially when non-lethal surveys have been shown to be sufficient for scientific needs,” said the group’s senior program manager, Alexia Wellbelove.
Japan is a signatory to the International Whaling Commission, which has maintained a moratorium on hunting whales since 1986.
But Tokyo exploits a loophole allowing whales to be killed for “scientific research” and claims it is trying to prove the population is large enough to sustain a return to commercial hunting.
It makes no secret of the fact that whale meat ends up on dinner tables.
Japan has hunted whales for centuries, and their meat was a key source of protein in the immediate post-World War II years when the country was desperately poor.
But consumption has declined significantly in recent decades, with much of the population saying they rarely or never eat whale meat.
In 2014, the International Court of Justice ordered Tokyo to end the Antarctic hunt, saying it found permits issued by Japan were “not for purposes of scientific research”.
Tokyo cancelled the hunt the following year, but resumed it in 2016, also killing around 300 minke whales.