Ahead of the so-called Castor transport the activists squabbled with police in the Baden-Württemberg city of Karlsruhe. Officers reportedly used pepper spray to disperse the crowd occupying the train tracks.
Protestors reported a number of injuries.
About 400 activists took part in the protest, according to police, but anti-nuclear groups said 700 were involved.
Activists declared the gathering a success after delaying the transport for several hours.
The train left the inoperative reprocessing facility there around 3:40 am and had reached the state border by 6:30 am, police said. The transport is headed north to the city of Lubmin in the state of Mecklenburg-Western Pomerania, where it is expected at an intermediate storage site on Thursday.
Some 56 tonnes of highly radioactive liquid waste is reportedly contained in the transport.
Protestors said they were against moving the dangerous substance from its point of origin to another part of Germany.