Japan has called on Australia, New Zealand and the Netherlands to take "effective measures" against the anti-whaling group, Sea Shepherd.
Foreign Minister Seiji Maehara said a strong request had been conveyed to the countries' ambassadors, where the group use ports and register their ships.
Japan cut its annual Antarctic whale hunt short earlier citing "harassment" by the environmental activists.
Commercial whaling was banned in 1986. Japan says its hunting is for science.
Japan uses a regulation permitting hunting for scientific research.
Iceland and Norway have lodged official objections to the ban and continue to hunt commercially.
Japan stopped its whale hunt on Friday, saying "harassment" by the US-based Sea Shepherd activists had made it impossible to continue.
The hunt had been halted temporarily last week, after Sea Shepherd boats blocked the stern of Japan's mother ship, preventing any harpooned whales from being loaded on.
Sea Shepherd has been chasing the Japanese fleet for weeks in the icy seas of Antarctica. Japan's fisheries minister said the group's actions made it "difficult to ensure the safety of the crew".
Japan's foreign minister said it was "extremely regrettable" that Sea Shepherd was not stopped.
Mr Maehara said the foreign ministry had called in envoys from Australia, New Zealand and the Netherlands to "convey a sense of regret and reiterate a strong request to take effective measures to avoid the recurrence of Sea Shepherd's obstructionist activities".
The environmental group operates Dutch and Australian-registered ships. It also uses ports in Australia and New Zealand for its campaigns.
Sea Shepherd founder Paul Watson described Japan's decision to call off its hunt "great news" but said activists would tail the fleet until it was out of the Southern Ocean whale sanctuary.
"Personally I don't trust them but I will take their word on this and we will follow them out. We're just not going to leave them until we know for sure they're out of the Southern Ocean," Mr Watson said.
Japan's fleet involves 180 people on four ships, and is entitled to kill up to 945 whales in Antarctic waters during the southern winter season.
Japan says the aim is to study their impact on fish stocks.
Few Japanese eat whale regularly, but many object to what they see as unjustified foreign interference in a cultural tradition, the BBC's Roland Buerk in Tokyo reports.
Anti-whaling nations, led by Australia and New Zealand, and environmental groups say the hunts are cruel and unnecessary.
Australia is taking legal action in the International Court of Justice against Tokyo over whaling.