Prime Minister Tony Abbott says any attempt by Japan to resume whaling in the Southern Ocean would not damage a "special friendship" underlined today by the signing of a free trade deal.

Japanese prime minister Shinzo Abe says his country will abide by the International Court of Justice's (ICJ) ruling earlier this year that its whaling program in the Southern Ocean must cease.

The ICJ ruled the program was not carried out for scientific purposes.

But Mr Abe, who is in Australia for a three-day visit, indicated that might not be where the matter ends.

"The decision by ICJ confirms that one of the objectives of the international convention for regulating whaling is indeed a sustainable use of resources," he said through a translator.

On Monday, Mr Abe indicated his intention to restart Japan's Southern Ocean whaling program.

He said Japan is committed to carrying out scientific research on whales.

"Japan, looking at international law and scientific ground, will engage in research of whaling in order to collect the indispensible scientific information in order to manage the whale resources," he said.

Mr Abbott says the two countries will have to differ on the issue.

"Friends can disagree. That's in no way inconsistent," he said.

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On Tuesday night a gala dinner was held at Parliament House in Canberra to honour Mr Abe.

Labor's foreign affairs spokeswoman Tanya Plibersek planned to raise the issue when she met Mr Abe at the dinner.

"Being such close friends does allow us to raise issues like whaling, where there has been some differences of opinion between Japan and Australia, and we will do that in the meeting," she said.

"I think the fact that Japan has accepted the international verdict on the current whaling program in the Southern Ocean is a very important step and a very good indication."

Earlier, Mr Abe and Mr Abbott signed three treaties designed to further liberalise trade and enhance cooperation in the areas of defence, science and technology.

Mr Abe also addressed a special joint sitting of federal parliament on the first full day of his visit to Australia.

Speaking in English, he reiterated his nation's vow of peace made after World War II, sending his condolences to Australians killed and traumatised in that conflict.

He said deepened economic and defence ties had led to a new era in the relationship between the two nations.

"We will now join up in a scrum just like in rugby," he said, drawing laughter from MPs.

"Let us walk forward together - Australia and Japan with no limit – yes, we can do it."

On Wednesday, Mr Abe will tour parts of Western Australia's Pilbara region.

Premier Colin Barnett will show Mr Abe and Mr Abbott the West Angelas iron ore mine, which is a joint venture project between Rio Tinto and two Japanese companies.

WA's exports to Japan totalled almost $23 billion in 2013, making the country WA's second largest export market.