Chief Cabinet Secretary Nobutaka Machimura has made the claim in response to the Coalition government's resounding defeat in the federal election.
Outgoing prime minister John Howard was an ally of Tokyo.
While in opposition, Labor called for legal action against Japanese whaling in Australia's Antarctic Whale Sanctuary, which is not recognised by other nations.
Japan's whaling fleet set out for the Antarctic Ocean just over a week ago despite renewed outcries from several countries, sparked by its plan to target humpback whales.
Japan, which says whaling is a cherished cultural tradition, abandoned commercial whaling in accordance with an international moratorium in 1986, but began what it calls a scientific research whaling program the following year.
Mr Machimura acknowledged the angry response from Australia.
"Humpback whales are very popular in Australia. I have heard that to catch and kill a humpback whale is a very emotional thing," he said.
"We have discussed this within the government, but for the moment we are continuing as planned."
Mr Machimura said Japan congratulated the new Australian government under Prime Minister-elect Kevin Rudd, and said he expected close ties to continue.
"Japan has maintained very good relations with Australia for a long time. We are strategic partners," he said.
"We had good ties with former Prime Minister Howard, and we think we can maintain this with the new Rudd administration. There is no room for doubt on this."
However, Japanese media said some officials have privately voiced concern about Mr Rudd, formerly a Beijing-based diplomat and the first Western leader to speak fluent Chinese.
The conservative Sankei Shimbun said Mr Rudd's election "carries risks" for Japan as he is expected to focus on China, which has uneasy relations with Japan.
But Mr Machimura said he expected few differences after Mr Rudd's decisive victory over Mr Howard.
"I understand that the new Australian administration maintains the current diplomatic and economic policies, although there may be some changes in policies concerning Iraq and the Kyoto Protocol," Mr Machimura said. © 2007 Australian Broadcasting Corporation