The Sea Shepherd anti-whaling group says the government is threatening to charge them about $200,000 in taxes if they don't take their ships to another country before returning to Australia to refuel.
Speaking in the Southern Ocean, where he is looking for Japanese whalers, Sea Shepherd activist Paul Watson lashed out at the Australian government.
"Their latest thing is that we can't come back to Australia to refuel unless we go to another country first, which means we would have to go one week out of our way to get to New Zealand and come back," Mr Watson said.
"If we don't, they will charge something like $200,000 on taxes on the fuel that we took," he said.
Each year Sea Shepherd confronts Japanese whalers in the Southern Ocean, pelting whalers with stink bombs and fouling propellers of Japanese vessels with long ropes.
Mr Watson said the Australian government was "passive aggressive" towards his organisation.
"They can't be too hostile because we have a lot of public support, but they are constantly hitting us," he added.
He said former environment minister Peter Garrett had stabbed his organisation in the back after Sea Shepherd originally lobbied for his election.
The former Howard government was more supportive of his group than the current Labor administration, he said.
"This government has been extremely hostile from the beginning," he said.
Mr Watson said he spoke with Environment Minister Tony Burke recently and asked the minister whether an Australian vessel could be sent down to the Southern Ocean to protect them.
"He said it is not going to happen," he added.
Meanwhile, two members of Sea Shepherd's Cove Guardians staying near Taiji, Japan, have been arrested.
The three US citizens were detained and stripped of all electronics and communications equipment except their personal mobile phones during a police raid, Mr Watson said.
He told AAP the police in Japan were one-sided, and could hold the members of Sea Shepherd for 23 days without laying charges.
The raid in Japan followed the arrest of a Dutch activist at the Dolphin Resort Hotel in Japan on December 16, who had been filming the transfer of dolphins from the sea to a holding pen, Sea Shepherd said.
Customs confirmed the Sea Shepherd would have to pay duty and GST on fuel if it did not complete an international voyage.
It could not say how much that would cost.
The taxes would also apply to any other stores on board the ship.
The Customs Act defines an international voyage as a ship visiting a place outside Australia, not including any outside waters.
"Therefore, if the ship only travels to areas of waters outside Australia, it is not deemed to have been on an international voyage for the purposes of ship's stores (which include fuel)," a Customs spokeswoman said in a statement to AAP.
"Leaving from Australia, sailing in the Southern Ocean and then returning to Australia, does not involve travel to a place outside Australia and is therefore not an international journey.
"When the ship returns to Australia, duty and GST would be payable on the ship's stores consumed while not on an international voyage.'
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