BNFL described the protesters' actions as "lunacy" and said Greenpeace had "endangered lives."
Greenpeace's "Nuclear Free Flotilla" caught up with the British-registered freighters, Pacific Pintail and Pacific Teal, with about 495 pounds of plutonium on board, in international waters in the Tasman Sea around dawn Monday.
New South Wales Senator Ian Cohen and another protester threw themselves into the water just 450 yards in front of the oncoming ships, brandishing a "Nuclear Free Pacific" banner.
Cohen, who jumped into the water with his trademark surfboard, said the protest had been "fantastic" and a triumph for "Aussie surfboard diplomacy."
"The Zodiacs (high-speed rubber boats) were out there chasing the boats for about seven hours and catching them and getting a protest out there in the middle of nowhere was brilliant," he told Reuters by ship-to-shore telephone.
The nuclear ships are currently about 625 miles east of the Australian mainland and heading south around Tasmania and west around Australia and out across the Indian Ocean.
BNFL hit back at Greenpeace, saying the protesters who had jumped into the sea had endangered not only their own lives but the lives of others.
"To throw themselves into the water in front of the vessel is the height of maritime lunacy and does Greenpeace no credit whatsoever," BNFL spokesman Mark Scott said in a statement.
"They should be condemned for their stupidity."
The Australian Democrats, Greens and Greenpeace have all said the shipment put the Australian mainland at risk but a spokesman for Australian Foreign Minister Alexander Downer said the government was satisfied about security.
"The appropriate safeguards are in place and the shipment entirely complies with international law. Australia has no position to object," he said.
But New Zealand is unhappy and has ordered its air force to track the ships.
"The government has made clear its opposition to such shipments and, as expected, as with previous shipments, the vessels seem to be staying well clear of New Zealand's 200-mile exclusive economic zone," said New Zealand Defense Minister Mark Burton in a statement.
The shipment is destined for the British reprocessing plant at Sellafield on England's northwest coast. The government in Ireland, whose coastline is just 110 miles across the Irish Sea, has long campaigned for the plant's closure.
The controversial shipment comes at a time when British Energy Minister Brian Wilson has published a policy paper outlining plans to reform the creaking nuclear power industry.
A new state agency would be responsible for paying to clean up existing waste
sites and mothball old plants, taking on huge liabilities from BNFL in what industry
experts see as a move toward privatizing the remaining profitable bits of the