The two groups were involved in dangerous collisions during the past whaling season, each blaming the other for ramming.
One serious incident was caught on video, with both sides releasing footage of a collision.
Japan's fleet is yet to depart for the annual hunt, which it says is legal under a scientific provision of the international whaling convention.
Sea Shepherd is readying for its 10th Antarctic campaign, with the ship Bob Barker due at its final port of Hobart this weekend.
Skipper Peter Hammarstedt says the vessel was rammed several times by the 8000-tonne factory ship Nisshin Maru.
"We're facing a very desperate adversary in the Japanese whale poachers," he told reporters in Hobart," Mr Hammarstedt said.
"The reason for that is it's a dying industry that we've already bankrupted three years in a row.
"Last year was the most aggressive that the Japanese whale poachers have ever been towards us.
"My feeling is that these poachers are criminals and we expect that we will treat them like the criminals that they are."
Last summer's incidents were reported to the Australian Maritime Safety Authority, the green group says.
It says the government should stick by an election commitment and send an Australian Customs vessel to enforce a 2008 Federal Court ruling that whaling in Australian waters is illegal.
"Last year we saw a whale harpooned 60 nautical miles off the Australian Antarctic coastline.
Sea Shepherd claims to have saved 932 whales and restricted Japan to nine per cent of its target catch in the past season.
An International Court of Justice decision on Australia's case against Japanese whaling is expected soon.