The Japanese government says Sea Shepherd activists have not put an end to this year's Southern Ocean whale hunt.
The whaling fleet has been between its ship and two Sea Shepherd boats.
Sea Shepherd hailed the suspension as a victory, saying with so little of the whaling season remaining Japan's hunt is effectively over.
But the Japanese consul-general in Melbourne, Hidenobu Sobashima, insists that is not the case.
"What was decided was temporary suspension of refuelling activities," he said on Thursday.
"Not more than that, not less than that."
It said the attacks happened after they were ordered to leave the area by one of the boats in the Japanese whaling fleet.
It also claimed armed Japanese coastguards threw "concussion grenades" at activists on the ships.
Mr Sobashima says the activists were responsible for the collision.
"Our understanding is yesterday morning the Sea Shepherd vessels, the Steve Irwin, Bob Barker and Sam Simon, approached and collided with the Nisshin Maru, during Nisshin Maru's refuelling operation," he said.
"What Sea Shepherd is doing endangers the life and property of the crew of the vessels and also endangers the safe navigation of the sea."
Sea Shepherd and the Coalition have called on Environment Minister Tony Burke to dispatch a Customs vessel to the area at once.
"The Nisshin Maru collided with my vessel several times and I think we were about 15 to 20 seconds away from being rolled over completely," he said.
"They're losing tens of millions of dollars," he said.
"The world is against them, they know that. Nobody believes for a moment that this is scientific research, it's a commercial operation and so they're being condemned worldwide and I think they're desperate and increasingly more aggressive."
Australia's Maritime Safety Authority says it is investigating the incident.
In 2010 the Sea Shepherd ship Ady Gil sank after being hit by a whaling vessel.
Australia strongly opposes whaling and launched legal action challenging the basis of Japan's so-called "scientific hunt" in December 2010.
Japan claims it conducts vital scientific research using a loophole in an international ban on whaling, but makes no secret of the fact that the animals ultimately end up on dinner plates.