The Australian government on Thursday ordered an investigation into the collision between a Japanese whaling security ship and a boat run by the Sea Shepherd anti-whaling group in Antarctic waters.

Deputy Prime Minister Julia Gillard said the Australian Maritime Safety Authority (AMSA) would probe the incident, adding she was amazed there was no casualties in the clash on Wednesday for which each side blaming the other.

"It is clear emotions are running high and lives are at risk," she said.

"Having watched the video it deeply concerns me. It seems miraculous that lives were not lost."

The results of the investigation will be made public, Gillard said, calling for calm until all the facts are revealed.

"I am calling for calm heads, calm judgement and a greater understanding of the facts," she said. "We are strenuously opposed to whaling and strenuously opposed to violence at sea."

The Australian government would not be sending a boat to monitor activities in the whaling scene, but it would continue to take advice on the situation as it unfolds, she said.

She added if the situation is not resolved diplomatically legal action may need to be considered.