Jan Kuciak's murder sparked political fallout and fresh demonstrations in the EU state after the news portal he worked for revealed the journalist had investigated the political corruption.
A protest called by a conservative opposition party drew about 1,000 people in the capital of Bratislava.
Many held candles, marching in silence in sub-zero weather in memory of Kuciak, who was murdered along with his fiancee.
Others carried banners saying "Mafia get out of my country" and used candles to spell out "Kuciak RIP" in front of the government building.
"We are here to show that Slovakia belongs to us and not the mafia," Igor Matovic, the leader of the opposition OLaNO party, told the crowd.
Hundreds of people gathered in the centre of Bratislava, Slovakia to remember Jan Kuciak. Source: CTK
The march was the first of several planned to honour Kuciak and protest against graft.
Leftist Prime Minister Robert Fico accused the opposition of using the murder as a "political tool to get people out on the streets and gain power."
An article by Kuciak published Wednesday by aktuality.sk focused on fraud cases involving Italian businessmen linked to Fico's entourage and forced two close associates to resign, while one minister quit in protest.
Maria Troskova, a close Fico aide, was forced out after Kuciak alleged she had ties to Italians purportedly involved with the 'Ndrangheta crime syndicate.
Kuciak, 27, and his fiancee Martina Kusnirova were found shot dead on Sunday at his home in Velka Maca, a town east of the capital Bratislava, raising concerns about media freedoms and corruption in Slovakia.
'Mafia in Slovakia'?
At the stroke of midnight, aktuality.sk and other Slovak media published Kuciak's last, unfinished investigative report on possible political links to Italian businessmen with alleged ties to Calabria's notorious mafia supposedly operating in eastern Slovakia.
"Italians with ties to the mafia have found a second home in Slovakia. They started doing business, receiving subsidies, drawing EU funds, but especially building relationships with influential people in politics -- even in the government office of the Slovak Republic," Kuciak wrote.
People place light tributes during a silent protest in memory of murdered journalist Jan Kuciak and his girlfriend Martina Kusnirova in Bratislava. Source: AAP
Troskova, 30, and Fico's crisis management officer Viliam Jasan said Wednesday they had given up their posts for the duration of the murder investigation, but denied links to the crime.
"We categorically reject any connection with this tragedy," they said in a statement.
Culture Minister Marek Madaric, who is a member of Fico's SMER-SD social democratic party, quit in protest calling the murder "terrifying" and telling reporters that "after what has happened, I cannot imagine just calmly sitting in my minister's chair."
Slovakia's leading SME broadsheet had first revealed details of Kuciak's investigation into alleged mob operations in Slovakia on Tuesday.
The report triggered an angry rebuke from Fico, who showed reporters stacks of euro bills totalling the one-million-euro ($1.2-million) reward he has offered for information that could lead to the killers.
"Do not link innocent people without any evidence to a double homicide. It's crossing the line. It's no longer funny," he warned Tuesday.
Participants during a silent protest march in memory of murdered journalist Jan Kuciak and his girlfriend Martina Kusnirova in Bratislava, Slovakia. Source: AAP
'Brutal assassination'
The Kuciak shooting followed the October murder of campaigning Maltese journalist Daphne Caruana Galizia -- who exposed crime and corruption on the Mediterranean island -- in a car bombing.
Slovak Police commander Tibor Gaspar, who has said the motive was "most likely" related to Kuciak's investigative journalism, has warned that publishing details of the case could tip off suspects.
Political analyst Grigorij Meseznikov told AFP the murder and its possible links to the Slovak political elite "could prompt a political earthquake".
"A red line has been crossed. This case could shake the electorate of the governing SMER-SD party to its foundations."
Fico, who once told journalists they were "dirty, anti-Slovak prostitutes", met the editors of top media outlets Tuesday to assure them of government commitment to the "protection of freedom of speech and the safety of journalists".
Other anti-corruption protests are being planned across Slovakia and in Prague, London and The Hague for Friday.
Thousands of mostly young Slovaks joined similar rallies last year demanding the dismissal of senior government and police officials for alleged foot-dragging on fighting graft.
Transparency International ranks Slovakia as the seventh most corrupt EU member.
