The $3.87 million campaign begins just ahead of Japan's Southern Ocean summer whaling season, when its fleet regularly kills more than 1,000 whales for research. Critics say the hunts are a cover for commercial whaling, banned since 1986.
The Australian campaign will invest in aerial surveys, satellite tags and genetic studies.
Environment Minister Peter Garrett said researchers do not need to use "grenade-tipped harpoons."
"Australia does not believe that we need to kill whales to understand them," Garrett said.
The fund will also carry out an assessment of Japan's scientific whaling program.
Japan's Fisheries Agency said last week that its whaling fleet is expected to cull up to 935 minke whales and 50 fin whales this season.
Japan kills the whales under a scientific program that Tokyo says provides crucial data on populations, feeding habits and distribution of the mammals in the seas near Antarctica and the north Pacific Ocean.
The research hunts are allowed by the International Whaling Commission, but opponents - including Australia and New Zealand - say they are killing the whales for commercial purposes. The meat is sold for food and ends up in restaurants.
The Japanese have hunted whales for centuries, and whale meat was widely eaten in the lean years after World War II. However, it has plunged in popularity in today's prosperous Japan.