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Emergency services were deployed to Bonn's central station on Saturday night after clashes between "left-wing and right-wing groups," police told German news agency dpa.
The western German city's station was temporarily closed, with roads blocked and rail traffic suspended in both directions.
Police said some people fell down onto the train tracks during the scuffles, but that no one had been injured.
The violence followed an annual demonstration by neo-Nazi activists in Remagen, about 23 kilometers (14 miles) south of Bonn. Police said around 130 people had taken part in the afternoon event, while up to 900 others had joined a counterdemonstration.
The fighting broke out at around 6 p.m. local time (1700 UTC) when a train carrying a number of protesters pulled into Bonn.
Authorities said they had launched investigations into serious breaches of the peace, among other charges.
Around 13,000 people attended a demonstration in the German city of Hamburg on Saturday to call an end to animal testing.
The protesters were aimed predominantly at the Labaratory of Pharmacology and Toxicology, a company that has been accused of abusing dogs and monkeys.
Its lab is based at Mienenbuettel, near Hamburg.
Read more: What is the future of animal testing?
"There is room for every animal. The civilian population will not allow these animals to be sold off and killed," said Friedrich Mueller, a member of SOKO Tierschutz, an animal protection group that co-organized the demonstration.
One activist obtained video footage of screaming monkeys and dogs covered in blood after he accessed the facility while posing as an employee.
It is not yet clear whether the LPT lab will be shut down. The local authorities say they do not yet have sufficient grounds to do so.
dpa contributed to this report