Several hundred people tried to get into the Reichstag building during a rally against coronavirus rules in Berlin on Saturday.
“This right to demonstrate peacefully is of course a very valuable asset even during a pandemic,” Merkel's spokesman Steffen Seibert said at a government press conference in Berlin.
However, he said their actions were “a clear abuse”.
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“The result was disgraceful images at the Reichstag which are unacceptable, anti-democrats trying to make themselves heard on the steps of our democratic parliament,” he said.
Police estimated 38,000 people, double the number expected, gathered in Berlin on Saturday to protest at restrictions imposed to curb the spread of the coronavirus, such as wearing masks and social distancing.
A protester standing naked in front of the Reichtag on Saturday. Photo: DPA
Several hundred broke through barriers and a police cordon to climb the steps leading to the entrance to the Reichstag.
They were narrowly prevented from entering the building by police, who used pepper spray and arrested several people.
Merkel praised as “quick-witted and brave” three police officers who were seen pushing back crowds from the entrance to the Reichstag alone until reinforcements arrived.
President Frank-Walter Steinmeier on Monday invited the officers to Berlin's Bellevue Palace to thank them for their work.
Steinmeier described the protesters' actions as “despicable”, adding: “We will not tolerate any anti-democratic smear campaign or disparagement of the
Federal Republic of Germany at the Bundestag.”
About 300 people were arrested in scuffles with police, in front of the Reichstag but also outside the Russian embassy, where protesters pelted police with bottles.
Resistance to coronavirus restrictions in Germany has gathered pace in recent weeks with demos attracting a diverse crowd of conspiracy theorists, anti-vaxxers and far-right or far-left activists.
Health Minister Jens Spahn was spat on at the weekend as he tried to talk
to protesters in the northern city of Bergisch Gladbach.
Seibert condemned the incident, saying it was “certainly not democratic dialogue”.