The train arrived at Dannenberg for unloading just after 4 am after leaving nuclear giant Areva's rail yard at Valognes, north-western France on Wednesday and being delayed by a string of obstacles set by anti-nuclear activists.
From Dannenberg rail station, its cargo of 11 containers of waste was due to be unloaded onto trucks, a process likely to take several hours.
Then it will begin the final 20-kilometre (12-mile) leg of the journey by road to the Gorleben storage facility, a former salt mine, on the River Elbe.
German police battled thousands of anti-nuclear protestors on Sunday, many chained to railroad tracks as they tried to block the train.
Thousands of activists swarmed the tracks along the route near the train's final destination in Dannenberg and boasted that the train had taken longer for its journey than the 92-hour record set last year.
Police said they detained about 1,300 people, including some who had chained themselves to the rails, requiring tricky and time-consuming operations to free them before the train could slowly rumble on.
About 150 people were injured in clashes, most of them demonstrators, according to security forces.
Monday's final road stage of the journey is also likely to be delayed by protest action, with campaigners already gathered near the Gorleben site.
Organisers said on Sunday about 23,000 protestors had gathered in Dannenberg, while police put the number at 8,000. About 20,000 police had been deployed along the train's German route.
The nuclear waste was produced in German reactors over the last few years and was then reprocessed in France before beginning its return journey last week.
The protesters argue that the shipment by train of spent fuel rods is hazardous and note that Germany, like the rest of Europe, has no permanent storage site for the waste, which will remain dangerous for thousands of years.
They are also angry that a pledged German phase-out of nuclear power, hastily agreed this year in the wake of the Fukushima disaster in Japan, will take another decade to implement.
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The demonstrators had travelled from across Germany as well as other European countries, while the large group in Dannenberg heard from Fukushima residents who spoke of what has been happening there.
There were outbreaks of violence on Thursday and Friday near Gorleben where 10 masked rioters attacked police with bricks and smoke bombs before managing to escape. Police said unidentified assailants hurling Molotov cocktails Friday damaged two patrol cars, while protestors have complained of excessive policing methods.