The train left for Wuerzburg in Bavaria in southern Germany after police managed to dislodge the protesters on Saturday evening.
"This action was prepared, we shall conduct an inquiry," Joerg Zenner of the German police told German television.
Hundreds of protesters have attempted to block the line at several points. In one incident, demonstrators set fire to barricades on the track.
On Saturday, thousands of people demonstrated near the nuclear waste disposal centre at Gorleben.
Wolfgang Ehmke, a spokeman for the People's Initiative for Ecological Protection, said that the group had protested for 31 years against nuclear waste being stored in Gorleben.
"Scientists say it is very dangerous to have a plant here, as the soil stock is in contact with water," he told Al Jazeera on Sunday.
"The government originally wanted to stop the production of nuclear energy, but the nuclear industry wants to carry on. Angela Merkel [Germany's prime minister] thus wants the industry to go on, although the opposition Social Democrats want to put all this to a stop.
"The demonstration here yesterday was a good day. We were supported by the Social Democrats, the Green party and the Socialists - we are very proud because we now know that we belong to the political mainstream."
About 14,000 demonstrators converged on the site, police said, with protest organisers saying that 16,000 people had turned out.
About 500 demonstrators took part in an overnight sit-in at the site, pledging to protest when the waste arrives on Monday.
Spent fuel from Germany's nuclear power plants is sent each year to France and Britain for reprocessing and then is returned to the Gorleben site.
The waste consignment is the 11th this year to be transported from La Hague to Germany.
In 2003, the German government set a two-decade timetable for closing the country's nuclear power plants.