The Ady Gil remained afloat, allowing the six crew members to salvage valuable equipment before being picked up by the Sea Shepherd Conservation Society vessel Bob Barker.
Both sides blame the other for the collision.
Ady Gil crew member Laurens de Groot said there was no doubt in the crew's mind that the Shonan Maru changed direction to target the Ady Gil.
"It came for the port side at full speed," he said.
"I think the captain was so pissed off with us (trailing him) that he wanted to come really close to maybe scare us off a bit but he's misjudged it and run right over us."
Glenn Inwood, a New Zealand-based spokesman for the Institute of Cetacean Research, the Japanese government-linked body that carries out the annual whale hunt, said video footage shot from the whaler showed the conservationists' boat moving toward the whaler just before the collision.
"The Shonan Maru steams to port to avoid a collision. I guess they, the Ady Gil, miscalculated."
The Ady Gil was a New Zealand-registered vessel but the clash occurred in Australian search and rescue territory so authorities from both sides of the Tasman would be involved in untangling matters.
However, final responsibility for the investigation would rest with Maritime New Zealand, Mr McCully told Radio New Zealand.
He said he would be taking up the matter with the Japanese government today.
"The New Zealand Government is totally opposed to Japanese whaling taking place in southern oceans but we're also opposed to killing human beings down there as well, and it is quite clear that unless there is some restraint exercised there is serious risk to human life in that region at the moment."
Despite strong differences on the whaling issue, he said that the Government worked constructively with Japanese authorities because there were issues of safety and welfare at stake.
Meanwhile, the shocked crew of the Ady Gil were working on how to salvage the multi-million dollar vessel, which was now tied to the Bob Barker.
There were hopes that it could be towed to the French Antarctic base Dumont Durville where there was a supply ship equipped with a crane which could lift the Ady Gil aboard, Mr de Groot said.
Plans had not been finalised, but if they were given the go-ahead, it would take 36-48 hours to reach the base.
Current conditions and the forecast for the next few days were favourable, he said.
Each southern summer the Japanese whaling fleet travels to Antarctic waters for what it calls a scientific whaling programme. Conservationists and many countries say the programme is a front for commercial whaling and want it to stop.
Yesterday's clash was the most serious in the past several years, during which the Sea Shepherd organisation has tried to harass the Japanese fleet into ending its whaling operations.
Mr Inwood said that Japan would continue to use its vessels to protect its crew in "whatever way it can".
The clashes were likely to continue until Sea Shepherd pulled out from its protest action, he said.
Video released by Sea Shepherd
- NZPA
