Riot police were deployed to guard the building in the capital Bratislava and fired teargas at the protesters, local media reported.
Some protesters chanted "Gestapo" and one carried a banner declaring "Stop corona fascism" over a draft law that would give people who have been vaccinated against COVID-19 easier access to public events and spaces than those who have not.
One policewoman was slightly hurt, Slovak media quoted parliamentary speaker Boris Kollar as saying.
The protest continued peacefully and eventually dwindled after the police intervention.
The European Union member state of 5.5 million has been struggling to get people vaccinated against COVID-19.
As of Thursday (July 22), just 34.9% of the population was fully vaccinated, data from Johns Hopkins University showed, which is one of the lowest vaccination rates per capita in the EU.