The Reichstag is the “symbolic centre of our democracy”, Interior Minister Horst Seehofer told Sunday's edition of the Bild newspaper. “It is unacceptable to see extremists and trouble-makers use it for their own ends.”
Police said about 38,000 people, double the number expected, had gathered in Berlin on Saturday to protest against restrictions imposed to curb the spread of the coronavirus, such as the wearing of masks and social distancing.
Late Saturday, several hundred protesters broke through barriers and a police cordon to climb the steps leading to the entrance to the Reichstag.
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They were narrowly prevented from entering the building by police, who used pepper spray and arrested several people.
The Reichstag, where German deputies meet, has a powerful symbolic role in the country.
The building, with its famous dome, was burnt down by the Nazis in 1933 in an act aimed at destroying what remained of German democracy between the two world wars.
“Plurality of opinions” is a “characteristic of the good functioning of society,” said Seehofer. But “freedom of assembly reaches its limits when public rules are trampled on.”
About 300 people were arrested in scuffles with police, in front of the Reichstag but also outside the Russian embassy not far from there in the city centre, where protesters pelted police with bottles.
Berlin city authorities had initially decided not to allow the Saturday demonstration to go ahead, fearing that the protesters would not keep a distance of 1.5 metres (five feet) apart or comply with face mask requirements.
The ban sparked outrage from organisers and their supporters who flooded social media with angry messages vowing to protest anyway, with some even calling for violence.
But on the eve of the demo, Berlin's administrative court sided with the demonstrators, saying there was no indication that organisers would “deliberately ignore” social distancing rules and endanger public health.
Protesters waved German flags and shouted “Merkel must go!”, a chant often used by the far-right Alternative for Germany (AfD) party against Chancellor Angela Merkel.
Some carried the flag of the German Reich which was used up until 1919.
“To see the flags of the Empire in front of the parliament is shameful,” tweeted Foreign Minister Heiko Maas.
The rally came as coronavirus cases continue to rise in Germany, with daily new infection numbers reaching highs not seen since April.
At a press conference on Friday, Merkel said confronting the virus will become more challenging in the coming autumn and winter months.
Merkel and the leaders of Germany's 16 federal states on Thursday introduced tougher coronavirus restrictions to curb the pandemic, including a minimum 50 euro ($59) fine for people caught not wearing face masks where one is compulsory.