The latest protests follow a government decision to limit access to indoor venues, such as nightclubs and restaurants, only to Covid-19 certificate holders.
The rally in Lucerne had not been approved by the local authorities but it passed without major incident.
Protesters temporarily held up traffic in one area of the city and allegedly abused some journalists who were reporting on the rally.
Police say they turned around 60 people away from the city centre and had to use pepper spray to break up a clash with other people who were opposed to the rally.
However, there were no immediate reports of injuries or arrests.
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Protesters march against Covid certificate
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More than 1,000 people demonstrated against extending the use of the Covid certificate in the Swiss capital, Bern, on Wednesday evening.
Swiss government limits access to restaurants to Covid certificate holders
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The government has extended the use of the Covid certificate to indoor public spaces such as restaurants, cinemas and fitness centres.
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