The Japanese government says its relationship with Australia is not at risk of being weakened, despite conflicts between whaling vessels and Sea Shepherd activists this week.
The Japanese have suspended refuelling of whaling ships after two Sea Shepherd protest boats were reportedly rammed on Wednesday when they tried to prevent refuelling in the Southern Ocean.
Japan's consul-general in Melbourne, Hidenobu Sobashima, says the two countries have good relations.
"We are aware of the difference of views on whaling, but ... our overall relationship between Australia and Japan is very cordial and cooperative and I hope we'll be able [to resolve] this issue in the future," he said.
But Mr Sobashima says it is regrettable that Japan's views have not been adequately reported in Australian media.
"Very few explanations on the part of the government of Japan appeared on the reports, that has been regrettable," he said.
On Wednesday Sea Shepherd said they were rammed after they had been ordered to leave the area by one of the boats in the Japanese whaling fleet.
It also claimed armed Japanese coastguards threw "concussion grenades" at activists on the ships.
Japan's fisheries agency has denied those reports, but confirmed one of its factory ships, the Nisshin Maru, rammed two boats belonging to Sea Shepherd.
Mr Sobashima says the activists were responsible for the collision.
Australia's Maritime Safety Authority says it is investigating the incident.
In 2010 the Sea Shepherd ship Ady Gil sank after being hit by a whaling vessel.
Australia strongly opposes whaling and launched legal action challenging the basis of Japan's so-called "scientific hunt" in December 2010.
Japan claims it conducts vital scientific research using a loophole in an international ban on whaling, but makes no secret of the fact that the animals ultimately end up on dinner plates.