The incident occurred as the dangerous cat and mouse battle between protesters and whalers continued, with Greenpeace reporting at least 20 minke whales had been slaughtered in the past 48 hours.

But the environmental activist group claimed some success, maintaining its tactics of harassment had allowed other whales to escape the harpoons.

Greenpeace expedition leader Shane Rattenbury said protesters' Zodiac inflatable boats were on the water trying to get between hunted whales and harpooners for the second day running, with whalers and protesters both having some success.

Mr Rattenbury said the stakes for whalers as the Antarctic clash entered its second week, were increasing.

He said 20 whales killed in the past two days meant the whalers were below the quota level required by the Japanese to fill its target numbers of 935 minke whales this summer.

No fin whales, a much larger species, had been seen slaughtered.

"We're refining our techniques. This wall of water we're using, where we spray the water into the air in front of the harpooner, is working well," he said.

"But then yesterday, at one stage, the pump that provides that wall of water ran out of fuel.

"Before we had a chance to refuel it, the harpooner took his shot and actually fired directly between two inflatable boats, which were not very far apart."

The harpoon did strike a whale, he said.

The whalers have repeatedly claimed that if an accident occurred during the confrontations, protesters hampering harpooners would be to blame.

Mr Rattenbury said the activists were on an emotional rollercoaster when on the water.

"We saw some of those horrible deaths yesterday," he said.

"We had a whale that was harpooned but was still trying to swim away, and that kind of thing.

"(But) there's the sense of exhilaration as you see some whales escape, because whales were escaping yesterday."

He said the catcher vessels typically chased a whale until it tired and was forced to spend more time on the surface, where it became an easier target.

"You can tell when a whale gets away. On a number of occasions yesterday, that did happen."

Mr Rattenbury said the wind in the area had risen, making the sea more choppy and difficult for inflatable boat crews.

"We are into what's going to be a difficult and drawn-out battle in the sense of this could go on for weeks - them continuing to try and hunt and us continuing to try and stop them," Mr Rattenbury said.

Meanwhile, the Greens called on the federal government to intervene following a claim by whalers that the protesters were being monitored by a United States anti-piracy agency.

Japan's Institute for Cetacean Research said yesterday the activities of Greenpeace and Sea Shepherd protesters were being monitored by the US Office of Naval Intelligence Civil Maritime Analysis Department's worldwide piracy report.

The report provides information on threats to and criminal action against merchant shipping worldwide.

Senator Brown said this required action from the federal government.

"The Japanese whaling fleet is an eco-criminal outfit which will bear full responsibility for any harm to Greenpeace protesters," he said.

He called on the federal government to explain the whalers' claims of piracy monitoring.