Under heavy police protection, the 12 containers of waste arrived aboard trucks at the Gorleben site, southeast of Hamburg.
Police earlier ended a sit-down protest by some 400 people on the road from a rail terminal at Dannenberg, where a train carrying the waste from a reprocessing plant at La Hague, France, arrived on Sunday.
They also removed three small groups of protesters who had chained themselves to concrete blocks on the road.
The transports are carried out under an agreement that sees spent fuel from Germany's nuclear power plants sent to France and Britain for reprocessing and then returned for storage.
Gorleben has been a traditional focus of anti-nuclear protests. In the past, shipments have led to clashes between thousands of demonstrators and police.
The protest movement has faded somewhat since the German government embarked in 2003 on plans to phase out nuclear power, but activists complain that the two-decade timetable for closing Germany's nuclear plants is too slow.