The Japanese organisation overseeing whaling operations in the Southern Ocean says it stands by its agreement with the conservation group Sea Shepherd to avoid confrontation.
Two Sea Shepherd vessels tracking Japanese ships say they are homing in on what they call the "slaughterhouse" ship, the Nisshin Maru.
The Institute of Cetacean Research reached an agreement last year with Sea Shepherd US, but it was unclear whether that covered Sea Shepherd Australia.
The institute said it did not wish to comment on the latest events in the Southern Ocean, but said its research programme conformed to a 2014 International Court of Justice decision and the International Convention for the Regulation of Whaling.
It confirmed it was targeting 333 black minke whales, but said the work involved what it called a "non-fatal investigation".