Japan's fisheries agency has told the ABC the country's whaling fleet is heading home after catching less than a third of its quota in the Antarctic.

Speaking to the ABC in Tokyo, the Japanese Fisheries Agency revealed the fleet finished its hunt three days ago.

The agency also confirmed the fleet caught 266 minke whales - less than 30 per cent of its quota.

The whalers also harpooned a single fin whale, despite having a quota of 50.

The Sea Shepherd conservation group, which harassed the fleet in the Antarctic, says it is a massive victory for whales.

Despite receiving a special budget boost of $30 million to fend off Sea Shepherd, the Japanese whalers were repeatedly obstructed by the activists.

Sea Shepherd activist Paul Watson says the whaling fleet's premature pullout is an unambiguous victory and it is high time the Japanese whalers learnt their lesson.

"This is the Southern Ocean whale sanctuary. What is it about the word 'sanctuary' they don't understand?

"You know you do not kill whales in a whale sanctuary."

Mr Watson believes that, sooner or later, Japan will realise it is wasting its money.

"I think it's been a very successful campaign. I predicted they wouldn't take over 30 per cent and they got 26 per cent so we were right on that one," he said.

"We chased them for 17,000 miles and took three of their three harpoon vessels out of the game so they really didn't have the opportunity to take that many whales."

'We'll be back'

Mr Watson says the whalers may be back next year, but so will Sea Shepherd.

"As long as they're going into the sanctuary, we will be there to protect the whales in this Southern Ocean whale sanctuary," he said.

"We'll be back next year with four ships. We're going to come with two scout vessels in the event that we lose one like we did this year.

"The scout vessels are the key. They'd hardly taken any whales if we hadn't have lost our scout vessel. But we'll be back stronger than ever."

He says he does not know how long the whaling battle will go on for.

"I'm hoping that this will be the last year, but I thought last year would be too. So it's really a question of how much money is Japan prepared to lose," he said.

The Federal Government says it welcomes Japan's decision to recall its whaling fleet from the Southern Ocean.

The Government says it remains opposed to commercial whaling, including Japan's so called "scientific" whaling program.

It says Australia will continue its efforts to achieve a permanent end to whaling through the International Court of Justice.