Federal Environment Minister Greg Hunt has confirmed Australia will again monitor Japanese whalers over the new year, as the fleet sails for its annual hunt.

Three vessels have left the port of Shimonoseki to join the factory ship Nisshin Maru on the passage south to hunt minke and fin whales, Kyodo news agency reported.

The departure means the fleet will likely reach the Antarctic towards the end of this month, as the government prepares to monitor it.

''Our commitment to monitoring the Southern Ocean this season is unchanged,'' Mr Hunt's spokesman said on Sunday. ''The minister met with the Japanese ambassador a few days ago and reaffirmed the government's position.''

Mr Hunt has said previously that it would be prudent and rational to ensure a Customs vessel was in the Antarctic during the whaling season, following clashes between the whalers and Sea Shepherd conservationists in past years.

Asked on Monday if Mr Hunt would send a Customs vessel to the Southern Ocean, a spokesman from his office said the Coalition had stated a commitment to monitoring whaling and that commitment stood.

He said beyond that commitment, the Coaltion would not pre-empt nor discuss operational activities.

Last season, whaling and protest ships repeatedly collided in waters of the Australian Antarctic Territory, as the Japanese fleet was held to its lowest ever kill - 103 whales.

Greens senator Peter Whish-Wilson said Australia's purpose-built Southern Ocean patrol vessel, the ACV Ocean Protector, was off the coast of Christmas Island, far from the whaling grounds.

''Why is the ice-rated ACV Ocean Protector being used as an expensive tropical water taxi for Immigration Minister Scott Morrison's Operation Sovereign Borders, when Minister Hunt has promised a vessel would monitor the whaling fleet in the Antarctic?'' Senator Whish-Wilson asked.

Sea Shepherd's three ships are expected to leave Melbourne and Hobart in about a week's time.

The government is hoping for a favourable decision from the International Court of Justice on Australia's plea to ban the hunt.