Environment Minister Peter Garrett said researchers did not need to use "grenade-tipped harpoons".
"Australia does not believe that we need to kill whales to understand them," Mr Garrett said.
The fund, to be spent by June, will also go towards developing opportunities for commercial whale-watching in the Pacific.
And an assessment will be carried out of Japan's "scientific" whaling program. The government says it will be independent and comprehensive.
Most of the $6 million will go to the Australian Marine Mammal Centre in Hobart.
The Australian Marine Mammal Centre was established as the first national research centre focused on understanding, protecting and conserving the whales, dolphins, seals and dugongs in our region. The Australian Marine Mammal Centre coordinates Australia's marine mammal research expertise to provide scientific research and advice to underpin Australia's marine mammal conservation and policy initiatives.
The Australian Marine Mammal Centre is based in Hobart in the Australian Antarctic Division's (AAD) Science Branch and has an extensive network of science members throughout Australia, representing over 20 institutions. A stakeholder advisory committee and a marine mammal scientific committee work with the Hobart-based Australian Marine Mammal Centre staff to review priority research needs and ensure cross-jurisdictional integration of the work program.
Given that the Rudd Government has not been successful thus far in stopping whale hunting in the Southern Ocean, the Minister's latest anouncement is very welcome.
Humpback whale tails image from the Australian Mammal Centre
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