Paul Watson, head of the Sea Shepherd mission, said the incident demonstrated a "continued escalation of violence" by the Japanese, following a collision which sank the activists' trimaran, the Ady Gil, on January 6.
"Because the whalers got away basically scot-free with the outrageous sinking of the Ady Gil, they now apparently think they can do whatever they want and they appear to have no qualms about endangering Sea Shepherd crew," Watson said.
"Australian and New Zealand lives are at risk every day in these waters," he said, referring to his mostly antipodean crew.
"What we really need is for the governments of Australia and New Zealand to step up and start enforcing maritime laws in these waters, or who knows what the whalers will do next."
Australia and New Zealand are investigating the collision between Japan's Shonan Maru No.2 and the Ady Gil, which caused the protest boat to break in two and sink without trace.
Australia expressed strong diplomatic concerns over the collision and claims the Japanese fleet chartered spying flights out of Australia.
Both the whalers and the protesters blame each other for the crash.
Japan hunts whales using a loophole in a 1986 international moratorium which allows "lethal research", and skirmishes with activists have grown increasingly sophisticated and intense.