The Federal Court has fined Japanese whaling company Kyodo $1 million for hunting whales within an Australian whale sanctuary, however there is little chance it will ever be paid.

Humane Society International (HSI) with help from the Environmental Defender's Office brought the case against Japanese company Kyodo Senpaku Kaisha.

They provided evidence of four occasions the whaling company caught minke whales within waters off Antarctica that are designated as a whale sanctuary by Australian environmental law.

Justice Jayne Jagot made a quick decision, finding the company guilty on all counts and fining them $250,000 for each occasion.

The company was not represented in court.

"We were surprised at the speed of things," Humane Society chief executive Michael Kennedy said.

"We thought we'd be in court all day. We thought we wouldn't get a decision until January sometime."

The case is the latest skirmish in a long-running legal battle against the Japanese whalers.

In 2008, HSI successfully took Kyodo to court where it was decided the whale hunt was against Australian law.

However the injunction against further whaling had no effect.

"[Kyodo] simply did not recognise the injunction; they did not recognise the law, because they don't recognise the Australian territory in the Southern Ocean," Mr Kennedy said.

The Australian Government won a case at the International Court of Justice in 2014 that found the Japanese whaling program was not "scientific" as they had always claimed.

'Significant question mark' over Australia's Antarctica claim

Kyodo has been fined $250,000 for each occasion it was found to caught minke whales. ( Supplied: Glenn Lockitch/Sea Shepherd )

The latest case argued that continued whaling was not only a breach of environmental law, but also showed contempt of the Federal Court.

Don Rothwell professor of law at the Australian National University said it was important to continue the battle as a matter of legal principle, but the court victory would likely also be ignored by the whalers.

"Successive Australian governments of both persuasions have declined to give effect to these relevant laws — notwithstanding the order of the courts," he said.

"The reason for that is they well know that if any attempt is made by Australia to arrest a Japanese whaling vessel or actually effectuate these orders, that will immediately provoke an international dispute with Japan.

"It won't necessarily be a dispute with respect to whaling but is is a dispute that will go to squarely to the legitimacy of Australia's claim over Antarctica and that is a dispute that Australia would seek to avoid.

"It needs to be acknowledged there is a significant question mark about the strength of Australia's claim over 42 per cent of the Antarctic continent," Professor Rothwell said.

Mr Kennedy said regardless of whether the company abides by the court's ruling, he is happy with the outcome.

"Japan always claimed it was doing its work legally. Well our court case in 2004, the ICJ in 2014, and now today proves that nothing they do in our view is at all legal," he said.

"This pressure is a thing that has to be kept up. At some point they must crack maybe this will be the final straw. That's what we're hoping."