The rallies in Bratislava and five other cities are part of a wave of protests that was fuelled by Prime Minister Robert Fico's trip to Moscow in December for talks with Russian President Vladimir Putin.
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Protesters have rallied in cities across Slovakia to condemn legislation approved by parliament that they say could curb free expression and hamper the work of nongovernmental organisations.
Protesters at Freedom Square in the capital Bratislava compared the measure to Russia's "foreign agent" law, which has been criticised as repressive, before marching to the presidential palace to urge President Peter Pellegrini to veto the bill.
"No to the Russian law," they chanted, and "Slovakia is Europe."
Parliament passed the measure on 17 April and it's supported by Prime Minister Robert Fico, who has frequently attacked NGOs.
Pellegrini, an ally of Fico, has not commented on the bill though recently he has questioned some of Fico's policies.
He has until 2 May to consider the legislation.
The measure would require, among other things, that NGOs publish reports with details on their leaders and any donors who have contributed more than €5,000 a year.
The government says the measure will make the financing and functioning of civil groups more transparent.
An analysis by Via Iuris, a non-profit organisation, said the law violates the constitution, including the right to privacy, freedom of expression and the right to freely associate, as well as European Union rules.
Its aim is to "stigmatise and limit the activities of civic groups," the group says.
The rallies in Bratislava and five other cities are part of a wave of protests that was fuelled by Fico's trip to Moscow in December for talks with Russian President Vladimir Putin.
Fico is planning to travel to Moscow again for a 9 May military parade to mark the 80th anniversary of Nazi Germany’s defeat in World War II.
No other European Union leaders have announced such a plan.
Protests in 20 other locations across Slovakia and abroad are planned for Friday, organisers said.
Fico, who is a divisive figure at home and abroad, returned to power in 2003 after his leftist Smer (Direction) party won a parliamentary election on a pro-Russia and anti-US platform.
His government has moved to overhaul public broadcasting to give the government control of public television and radio.
That, along with an amendment to the penal code to eliminate a special anti-graft prosecutor, critics say is evidence of Fico leading Slovakia down a more autocratic path.