As he was sworn in for his second five-year term last week, Milos Zeman used his inauguration speech to accuse public broadcaster Czech Television and other journalists of favouritism and bias.
Mr Zeman, who has been in office since 2013, blasted the press for criticising his anti-migrant and pro-Russia rhetoric.
He previously prompted controversy after he brandished a replica gun with the words “for journalists” inscribed on it during a press conference.
Around 4,000 people attended the rally in the capital’s Wenceslas Square on Wednesday, according to the protest’s organisers.
During the protest against Mr Zeman and the country’s Prime Minister, Andrej Babis, demonstrators waved flags, lit up their mobile phones and jingled their keys — a gesture used during the country’s communist era, when it came to symbolise the unlocking of doors and was used as a way of telling the communists to leave.
The square was previously the site of huge demonstrations against what was then Czechoslovakia’s communist government.
On Thursday, students from 200 schools across the Czech Republic gathered in further protests.
Mr Kuciak was investigating fraud cases involving politically-connected businessmen in Slovakia, which split from the Czech Republic 25 years ago.
Mr Zeman has previously referred to journalists as “manure” and “hyenas” and joked with the Russian President, Vladimir Putin, that some journalists at an event needed to be “liquidated.”
Press freedom is becoming a contentious issue in the Czech Republic, as ownership of the media becomes increasingly concentrated in the hands of a few wealthy individuals.
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