Australia's Department of Foreign Affairs and Trade announced on Friday that Japan resumed whaling in the Antarctic waters, days after it was forced to stop by groups of anti-whalers.

On Thursday the whale hunt restarted just as Australian Foreign Minister Stephen Smith arrived in Japan for a diplomatic visit.

He said that even though Australia is against whaling, the two countries “agree to disagree,” CNN reports.

On Friday he said: "Whilst we have a strong disagreement, this is not an issue, which in my view, is, or can, or will adversely impact upon the fundamentals of our partnership with Japan. I regard the resumption of whaling in the last couple of days as disappointing. We would prefer if it hadn't occurred, but that's as a consequence of the Australian government having a strong view that whaling should cease."

Australia’s claim to parts of the Southern Ocean as its territorial waters is not entirely recognized.

In the Southern Ocean Whale Sanctuary, which is a protected area of 19 million square miles surrounding the continent of Antarctica, the whale hunt for commercial purposes is not allowed.

But Japan claims that its plan to kill the 1,000 whales is for scientific purposes, while anti-whaling groups see them as poachers.

Last month Japan was forced to stop the whaling after two activists from Sea Shepherd boarded on a Japanese whaling ship trying to stop the hunt, but in the end the standoff ended with the two transported by a an Australian fisheries patrol ship.

Smith said: "These things occur. I regard this as a coincidence."

Prime Minister Yasuo Fukuda met earlier with Smith and said: "What is more important is not to make these things negatively influence diplomatic negotiations," Reuters informs.

For Japan, whaling is a cherished cultural tradition. In 1986 it abandoned commercial whaling due to an international moratorium.