Tokyo plans to issue a formal protest to the Netherlands, which licenses the activists' boat.
"Such interference is aimed at causing damage and causes fear for the safety of the ship and crew operating legally in international waters," Nobutaka Machimura, Japan's Chief Cabinet Secretary told reporters on Monday.
"We hear, as a fact, that four people were injured as a result and we cannot accept such action. The Japanese government strongly condemns such interference by the Sea Shepherd."
Sea Shepherd's leader Paul Watson described the incident as "non-violent chemical warfare".
|A handhout photo shows activists hurling |
chemicals at the whalers [Reuters/ICR]
In a statement released from on board ship he said the substances thrown at the Japanese ship were harmless, foul-smelling and slippery substances, designed to make it difficult to process whales.
"We only use organic, non-toxic materials designed to harass and obstruct illegal whaling operations."
Sea Shepherd's confrontational tactics have been criticised by other conservation groups such as Greenpeace which says the group risks causing injuries to humans in its efforts to stop the Japanese whale hunt.
Australia, which has been a vocal opponent of the Japanese whale hunt, also criticised Sea Shepherd's actions.
"I absolutely condemn actions by crew members of any vessel that cause injury or have the potential to cause injury to anyone in the high seas," Stephen Smith, the Australian foreign minister, told reporters.
Japan plans to slaughter a thousand whales this season in a hunt it says is for scientific purposes.