Japan's whaling body has accused anti-whaling activists of ramming the Nisshin Maru factory ship while it was trying to refuel in the Southern Ocean.
The Institute of Cetecean Research has released a statement criticising Sea Shepherd and described its actions as "malicious and unacceptable".
The whaling ship and the fuel tanker had to abandon the process after allegedly being struck five times by the Steve Irwin, Bob Barker and Sam Simon.
"On February 25 during refuelling operations, the Antarctic whale research mother ship Nisshin Maru and her supply tanker were subject to sabotage by the Sea Shepherd ships," the statement said.
"During their obstruction to refuelling operations the SS vessels rammed into, at the least: BB three times; SmS two times, with the NM and the supply tanker.
"In order to secure safety, the NM decided to interrupt her refuelling procedure due to the extremely dangerous and foolhardy behaviour of SS vessels.
"The sabotage is not only malicious but inconceivably obstructive actions. Thus it threatens safety of our research ships and lives of crews on them and is therefore completely unacceptable."
The statement also said no one was injured and that the damage was being assessed.
Director of Sea Shepherd, Doctor Bob Brown has denied the accusation.
"It is the factory ship that is closing in the tanker," he said. "To get close to it, to get refuelled, and that's what Sea Shepherd is preventing.
"The factory ship is illegally whaling, the fuel ship is illegally in Antarctic waters with heavy fuel oil."
The drama unfolded in the aftermath of the to the Southern Ocean to defend the whaling fleet, a claim Japan has denied.
The Australian Maritime Safety Authority says it has received incident reports from the Sea Shepherd.
The authority says it will investigate those related to the Sam Simon ship, as it is the only vessel sailing under an Australian flag.
Yesterday, Sea Shepherd claimed the 12,000-tonne vessel, the Shirase, had arrived to help whalers refuel.
The ship is from the Japanese Maritime Self Defence Force.
Federal Environment Minister Tony Burke says Japan denies a link between the icebreaker and the whaling fleet, but he wants to know if the ship is supporting or transferring Japanese personnel to the fuel tanker.
Dr Brown says one of the icebreaker's three helicopters was helping a Korean tanker gain access to the Nisshin Maru.
He added that he feared an escalation of violence between whalers and activists.
"I am concerned," he said. "It may be just a show of strength by Tokyo but in the past we've never been able to assume that's all that's happening.
"It's obviously part of Japan's unfolding plan to take control, the Japanese have been moving their navy into position.
"March is the end of it. This mission by the Japanese whaling fleet has been a massive financial and public relations failure.
"But the third failure coming along with this is the inaction of the Australian Government."
Last Wednesday, Sea Shepherd claimed the Bob Barker and the Steve Irwin were rammed by the Japanese vessel Nishin Maru.