Greenpeace said on its website that activists plan to put inflatable boats between the whalers' harpoons and the whales if the fleet begins operations.
"If they try to start whaling, then we will do everything that we can to take peaceful direct action to stop that," Sara Holden, an Esperanza crew member told Australian Broadcasting Corporation (ABC) radio.
Japan's whaling fleet plans to hunt 935 minke whales and 50 fin whales for research over the Antarctic summer.
It recently abandoned plans to hunt 50 humpback whales after international condemnation and a formal diplomatic protest by 31 nations.
Greenpeace has been searching for the whalers for 10 days and found the fleet in the early hours of Saturday by following krill, the marine shrimp which is the whales' main food.
An Australian fisheries ship last week also set out in pursuit of Japan's whaling fleet near Antarctica to gather evidence for an international court challenge to halt the annual slaughter.
The icebreaker Oceanic Viking, normally used for customs and fisheries policing, left a naval base near Perth on Tuesday to find and track the fleet in the Southern Ocean for almost three weeks.
Chris Bowen, an Australian finance minister, urged the Greenpeace activists to show restraint.
"Their own personal safety is at risk and the personal safety of others is at risk," Bowen said.
Japan has long resisted pressure to stop scientific whaling, insisting that the practice is a cherished cultural tradition.
Its fleet has killed 7,000 Antarctic minkes over the last 20 years.