After some 28 hours on the tracks, the so-called Castor transport reached the intermediate storage site at the town in the northern state of Mecklenburg-Western Pomerania.
The five containers full of highly-radioactive atomic waste would be moved to the storage facility within the next few hours, a spokesperson for the EWN energy group said.
The train left Karlsruhe in the southern state of Baden-Württemberg late on Tuesday, with protestors managing to delay its journey several times along the way. Some 300 activists were detained overnight on Tuesday for blocking the way.
On Wednesday night and early on Thursday demonstrators blocked the train's passage briefly again in Ludwislust, Schwerin, Ribnitz-Damgarten and near Stralsund.
In the final stretch of the journey police were forced to remove more than 50 people from tracks between Greifswald and Lubmin.
Several activists were injured during police operations to remove them. One demonstrator near Lubmin sustained abrasions after chaining himself to the railroad tracks, while another was injured during a clash with police.
Demonstrators said some came away with bloody noses and lips, and one member of the Mecklenburg-Western Pomerania Green party association called officers' behaviour “super brutal.”
There were also unsubstantiated reports of broken teeth.
Some 56 tonnes of the radioactive liquid waste was reportedly contained in the transport.
Protestors said they were against moving the dangerous substance from its point of origin to another part of Germany.