Japan's Antarctic fleet has resumed whaling after anti-hunt activists suspended their pursuit of the vessels in the Southern Ocean to refuel.
Japan says its whaling is for research purposes
Media reports say an Australian customs vessel saw five whales being harpooned and hauled on to a Japanese ship.
The Japanese fleet had stopped hunting for three weeks while it was pursued in Antarctic waters by the campaigners.
Australian Foreign Minister Stephen Smith held talks with his Japanese counterpart in Tokyo on the issue.
A ministry spokesman said Mr Smith had "expressed disappointment that whaling had resumed in the Southern Ocean".
He also "conveyed the Australian government's strongly held view that Japan's whaling programme should cease".
But the two had "agreed to disagree" on whaling.
Before the meeting, Japan's Foreign Minister Masahiko Komura told reporters the issue would "inevitably" be raised.
"Minister Smith may bring up the whaling issue, or I may bring up the harassment issue," he told reporters.
Australia has declared a whale sanctuary in parts of the Southern Ocean where the Japanese fleet has been, but Japan does not accept Canberra's authority.
As the protesters left the scene, a member of the Sea Shepherd group vowed to come back and continue harassing the whaling fleet.
"This is a retreat for supplies only. We have not surrendered the sanctuary to the whale killers," Paul Watson said.
The Japanese fleet plans to kill about 900 minke whales and 50 fin whales by mid-April as part of what it describes as a scientific research programme.
Other nations and environment groups say the research goals could be achieved using non-lethal methods, and call the programme a front for commercial whaling.