Two Greenpeace members, dressed in biohazard suits, threw themselves into the water in a bid to prevent the British registered Atlantic Osprey from docking at the Swedish port of Studsvik, some 100 kilometres south of Stockholm.
No arrests followed however, as the pair were fished out of the water by authorities and returned to Greenpeace.
Protestors are fighting the shipment over safety concerns.
Some 30 campaigners from the organisation, in six inflatable dinghies, had been waiting for the Atlantic Osprey to arrive in Studsvik.
The vessel was able to dock at Studsvik as planned.
While no date for the Atlantic Osprey’s departure has been announced, Greenpeace says it will remain at the port to monitor the loading process.
The waste originates from the decommissioning of a nuclear reactor used between 1954 and 1970 for research into atomic weapons and nuclear energy.
The reactor was decommissioned in 1982, producing 4.8 tonnes of spent nuclear fuel which was taken to Studsvik.
British and Swedish authorities agreed to ship the waste to Britain’s Sellafield reprocessing facility in 2005.