Australia's foreign Minister said the mission would be linked with several days of aerial surveillance.
Australia has long opposed Japanese whaling, but Kevin Rudd, the country's new Labor prime minister, has signalled a tougher stance than previous administrations by committing government resources to collecting evidence.
The Japanese whaling fleet plans to kill almost 1,000 whales this year in its annual hunt in the Southern Ocean as part of what it says is scientific research.
Most of the whales will be minke whales, while the fleet also plans to kill 50 larger fin whales.
|Environmental groups say research does not |
require killing of whales [Greenpeace photo]
In December, facing mounting international criticism, Japan announced it was shelving plans to add 50 endangered humpback whales to the list.
Commercial whaling has been banned since 1986, but Japan is allowed to kill a limited number of whales each year in the name of science.
Environmental groups dismiss those claims, saying any scientific study of whales can be carried out without killing them.
The whale meat from the hunt is sold in Japanese supermarkets and the proceeds used to fund further research missions.
Environmental groups Greenpeace and Sea Shepherd have each separately sent their own ships to track and harass the Japanese fleet, as they do each year, but have so far failed to find the whalers in the icy Southern Ocean.
Greenpeace has welcomed the departure of the Australian ship, but urged the government in Canberra to assist by giving it the location of the Japanese fleet, so its own ship could also monitor the whalers.
A spokesman for Japan's whaling mission said this week it was mid-way through its summer hunt.