The police say some 300 protesters threw stones and fireworks at security officers near the town of Dannenberg.
The protests occurred near railway tracks used to transport nuclear waste shipment reprocessed in France to a storage site near the town of Gorleben.
Some 20,000 officers are on hand in the region to keep the tracks open.
Officials have yet to resolve where the new load of nuclear waste from French nuclear energy plants should be stored permanently.
Activists say Gorleben is unsafe.
compiled from agency reports