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The troops boarded the sailing boat, snapped its sails and towed it into the Cherbourg military base where one of the two ships carrying the radioactive cargo is expected to arrive today.
Two other protesters were arrested after trying to scale the gates of the dockyard.
A Greenpeace spokeswoman said the demonstrators’ actions were “peaceful and non-violent” and added that the commandos had arrived in fast inflatable boats before cutting the sails and towing the boat in.
Shaun Burnie, a Greenpeace spokesman at Cherbourg, said the yacht which was stormed was owned by a French former Round the World yacht race winner, Eugene Riguidel, after it entered the military zone around Cherbourg port.
Those arrested were M Riguidel, John Castle from Guernsey, who is in his early fifties, and a Swedish protester, Pernilla Svenberg, 34, Mr Burnie said.
“They are being held in prison overnight, which obviously is regrettable but they are happy to have made their point,” Mr Burnie said.
Several small ships with activists have been positioned offshore in protest at the transit of the 125kg (275lb) cargo of plutonium, which would be enough to make 40 nuclear weapons, from Charleston in the United States.
Since Saturday, dozens of activists have awaited the arrival of the two British-registered ships, escorted by armed commandos, at Cherbourg.
Activists have questioned the safety of transporting such security-sensitive cargo at a time of heightened risk of terror attacks globally.
The French nuclear energy firm Areva, whose Cogema unit will recycle the plutonium, said that it would release information on the shipment from Charleston only a few hours ahead of its arrival.
The shipment is part of a post-Cold War agreement between the United States and Russia to get rid of plutonium from excess nuclear warheads.
Greenpeace criticised the transport, saying that on arrival in Cherbourg the plutonium would be driven more than 1,000 km (620 miles) in vulnerable lorries to a factory in southeast France.
Areva’s Cogema unit will recycle the plutonium into nuclear fuel at its Cadarache and Marcoule plants in southeastern France and ship it back to the United States, which plans to use it in an electricity-generating reactor.
It is part of the US Department of Energy’s controversial programme to turn plutonium from the “excess” nuclear warheads into mixed-oxide (MOX) plutonium-uranium enriched fuel.
Critics fear that the fuel could potentially be used to build nuclear weapons.
In July 1985, French special agents sank Rainbow Warrior, the Greenpeace vessel, in Auckland harbour in New Zealand, killing one of the environmental group’s photographers. The attack caused a major international rift between New Zealand and France, which later admitted its involvement.
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