Tokyo, however, is still going ahead with its expedition in the Antarctic, planning to kill nearly 1,000 other whales, mostly of the smaller minke species.
Machimura said Japan and Australia had cultural differences over whales but that Tokyo hoped to preserve relations with Canberra, where the new left-leaning government has stepped up pressure against the hunt.
"Australians consider whales to be very affectionate, something I can't really relate to. But apparently they give names to every whale and there's quite strong public sentiment," Machimura said.
But he denied that Japan was backing down in response to Australia, saying it made its decision after talks with the head of the International Whaling Commission (IWC).
"Japan is thinking of the IWC as an organisation as a whole and that is why we decided on this, instead of particularly thinking about Australia," Machimura said.
Japan, which says whale meat is part of its culinary culture, hunts whales using a loophole in a 1986 IWC moratorium that allows "lethal research" on the giant mammals.
In Canberra, a spokesman for Stephen Smith, the foreign minister, said: "The Australian government welcomed Japan's announcement.
"While this is a welcome move, the Australian government strongly believes that there is no credible justification for the hunting of any whales and will vigorously pursue its efforts ... to see an end to whaling by Japan," he said.
Meanwhile, the Australian embassy in Tokyo said it, along with other embassies, would deliver a document on whaling to Japan's foreign ministry on Friday.
The embassy has declined to disclose the contents of the document or say how many other countries were involved.
While the whales are killed for "scientific purposes", their meat ends up in Japanese supermarkets and restaurants, although the public appetite for what is now a delicacy is waning.
Some experts say Japan fears that limits on whaling will lead to limits on all Japanese fishing. Others argue the whaling campaign is a form of nationalist diplomacy.