The incident has forced Greenpeace to rethink their human shield style protest against Japanese scientific whaling in the Southern Ocean.
The Japanese says Greenpeace is taking the risks for the sake of public relations.
A harpoon from Japanese whaling vessel Yushin Maru No.2 was fired directly over the Zodiac inflatable boat, which was shadowing a minke whale in Antarctic seas.
Greenpeace chief executive Steve Shallhorn said the harpoon had flown within a metre of the inflatable.
"Greenpeace had been doing what it has been doing for three weeks – putting out inflatables between whales and harpoons," he said.
"The harpoon impacted on the whale but the towing rope got caught on our boat. And as the whale began to sink it put our boat in jeopardy. The rope got taut and threw one of our people into the ocean."
Canadian activist Texas Joe Constantine, the second mate on the Greenpeace ship Arctic Sunrise, struggled in the water for a short time before climbing back into the boat.
"He may have swallowed some seawater and whale blubber but he is all right," Mr Shallhorn said.
He said the whalers were becoming frustrated with the success of the protest and were starting to take more chances. But he said the new tactics would not deter Greenpeace. "They have killed far fewer whales then they would have without us being around."
Greenpeace spokesman Shane Rattenbury said the protesters had prevented the ship from harpooning the minke whale for over an hour, but the harpoon operator decided to fire when he believed he had a clear shot.
The Greenpeace spokesman said he feared the whalers were taking the confrontation to a new level. "Yesterday took it to a new level – we are very concerned about that," Mr Rattenbury said on Sky News.
"There is definitely an increasing level of tensions down here and the harpooners are certainly starting to take shots that perhaps a week or two weeks ago they would not have taken.
"So it is certainly forcing us to think about our tactics and we might have to look at a different way of doing things."
But Mr Rattenbury said Greenpeace was achieving results. He said it underlined the fact that more pressure was needed from governments to end the whale cull, which the Japanese say is for scientific purposes.
"There is a limit to what Greenpeace can do down here, and as the risks increase we really need to see the anti-whaling governments around the world take stronger action to bring this hunt to an end so we don't have to be putting ourselves in the firing line any more," Mr Rattenbury said.
"It's quite clear that this is not about scientific research – you don't need to kill a whale to study it. This is just commercial whaling in disguise."
The Institute of Cetacean Research (ICR) in Tokyo said Greenpeace was taking more and more risks to keep their PR campaign in the news.
"The fact that the rope fell onto their inflatable and one of the activists fell into the water is entirely their fault," ICR director general Dr Hiroshi Hatanaka said.
"We are also concerned that they tried to cut the line because it makes it more dangerous for them.
"Greenpeace are taking more and more dangerous risks to maintain media interest in their PR campaign.
"We continue to do our utmost to ensure the safety of the activists, but we cannot foresee their increasingly dangerous stunts."
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