The activists included members of Thügida, NPD and other right-wing groups who gathered at Berlin central station to protest Merkel's participation in the upcoming election and demand her resignation.
Many were holding banners, saying "Merkel must go" or "For the future of our children! Patriots of Rostock/ Ruegen/ Strahlsund."
On their way to Berlin's major Alexanderplatz square, the protesters encountered large groups of counter-demonstrators who tried to disturb their procession.
The counter-demonstration consisted of about 1,000 activists, holding placards with the inscriptions "We are against racism," "We do not want the AfD in our city," and "We want to live together and work in peace!"
Many Berlin residents joined the anti-populist demonstration and tried to disturb the protest campaign of right-wing supporters by throwing water and raw eggs out of their windows.
Commenting on the event, police spokesman Thomas Neuendorff said in an interview with Sputnik Germany that the demonstrations were generally peaceful with the exception of a couple of small fights between activists from different groups.
Right-wing forces have been on the rise in Germany since the outbreak of the refugee crisis in 2015, when hundreds of thousands of undocumented migrants entered the EU, raising security concerns and anti-migrant sentiments among the population.
Thus, the German populist Alternative for Germany (AfD) party won 14% of the votes during the September local parliamentary election in Berlin and became the fifth most popular party with 25 seats in Berlin's state parliament.
According to the latest polls, in the federal election of September 2017 AfD is expected to gain about 12 percent of the votes and become the third-largest party in the Bundestag, the lower house of the German parliament.