About 1,000 people turned out for the rally, which has become a weekly event in the German capital. Saturday's protest attracted mainly far-left activists but there were also right-wing supporters and members of other fringe groups.
Police put up barriers around Rosa Luxemburg square, where the protesters were headed, leaving the participants to gather in nearby roads.
The protest “is not in line with the rules” in place to prevent the spread of the COVID-19 virus, police said on Twitter, telling those taking part to disperse.
Some of the demonstrators wore T-shirts accusing Chancellor Angela Merkel of “banning life” while others simply called for “freedom”. Others brandished placards bearing slogans such as “Stop the pharmaceutical lobby”.
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The protest was unauthorised as a result of emergency rules in Berlin banning gatherings of more than 20 people. The protest organisers' website called for “an end to the state of emergency” and played down the threat posed by the virus.
Public discontent with the confinement rules has been growing gradually in Germany, as in other countries, though Merkel's popularity remains high.
She has received plaudits for her management of the health crisis which has seen Germany's COVID-19 toll — 5,500 according to an AFP tally — remain significantly lower than in Italy, Spain, France and Britain where the death tolls have all risen above 20,000.
Opposition to the lockdown measures is being led by the far-right, the main opposition force in the German parliament.
The far-right Alternative for Germany (AfD) party accuses the government of exaggerating the risk posed by the virus and has called for the immediate reopening of all businesses.