Officials blame harassment by animal-rights activists for the low catch, and vowed to press ahead with the hunt.
The hunt is allowed under international rules as a scientific programme despite the 1986 ban on commercial whaling.
Some protesters hurled containers of rancid butter and acid at the whalers, and the Japanese coast guard shot back "sound balls" similar to stun grenades.
In January, two Sea Shepherd activists jumped onto a Japanese ship and spent several days in detention on board.
Activists this week said even the reduced take of whales was too large, and called on Japan to renounce the hunt at the next meeting of the International Whaling Commission in Chile in May.
Tokyo has long argued that the whaling ban should only apply to endangered species.
It also accuses the West of hypocrisy for criticising current Japanese whaling after American and European whalers nearly wiped out the mammals in the 19th and 20th centuries.
The Japanese have hunted whales for centuries, and whale meat was widely eaten in the lean years after World War II.
The meat, however, has plunged in popularity in today's prosperous Japan.
Violence is ascribed to the protestors
The Australian Embassy had been advised by the Japanese that a crew member on board the Nisshin Maru fired "warning" shots at the anti-whaling group on board a ship named Steve Irwin.
"In addition to the lead bullet lodged in Captain Paul Watson's vest, up to seven flash grenades were also hurled by armed Japanese Coast Guard Officers, injuring two other Steve Irwin crew members," reported Peter Brown, officer on board Steve Irwin.