Slovakia will convene a state security council meeting and the cabinet will also meet on Thursday, the government office said.
Miriam Lapunikova, director of the FD Roosevelt University Hospital in Banska Bystrica where Fico is admitted, said the prime minister had undergone five hours of surgery with two teams to treat multiple gunshot wounds.
"At this point his condition is stabilised but is truly very serious, he will be in the intensive care unit," she told reporters.
Deputy Prime Minister Robert Kalinak said doctors had managed to stabilise Fico's condition overnight, and procedures were under way to secure further improvement.
Doctors have managed to stabilise Robert Fico's condition since the Slovak prime minister was shot. (AP PHOTO)
"Unfortunately the condition continues to be very serious due to the complicated nature of the wounds, but we all want to believe firmly that we will succeed in managing the situation," he said.
The shooting on Wednesday was the first major assassination attempt on a European political leader for more than 20 years, and spurred international condemnation, with political analysts and lawmakers saying it was indicative of an increasingly febrile and polarised political climate across the continent.
The gunman shot Fico, 59, during a visit to the central Slovak town of Handlova, initially leaving the prime minister in critical condition and undergoing surgery hours later.
Slovak news media reported the 71-year-old male shooter was a former security guard at a shopping mall, an author of three collections of poetry and a member of the Slovak Society of Writers. News outlet Aktuality.sk cited his son as saying his father was the legal holder of a gun licence.
In an undated video posted on Facebook, the alleged attacker was seen saying: "I do not agree with government policy."
"Liquidated mass media. Why is RTVS (public broadcaster) being attacked? Why are people ... Mazak, why has he been kicked out of his post," he continued, in reference to Jan Mazak who had been removed as chairman of a state judicial council.
Reuters verified the person in the video matched images of the man arrested after Fico's shooting.
Interior Minister Matus Sutaj Estok told a news conference on Wednesday that the attack was "politically motivated".
Slovak news media report the shooter was a writer and former security guard at a shopping mall. (AP PHOTO)
Fico and his government coalition allies have criticised sections of the media and the opposition, saying they had inflamed tensions in the central European state.
Slovakia's biggest opposition party, the liberal, pro-western Progressive Slovakia, called off a planned protest and called for restraint to avoid escalating tensions.
The country of 5.4 million has seen polarised political debate in recent years, including a hard-fought presidential election in April that helped tighten Fico's grip on power after his ally Peter Pellegrini won.
Since returning for the fourth time as prime minister last October, Fico has shifted policy quickly in what opposition critics said was a power grab threatening the rule of law.
His government has scaled back support for Ukraine while opening dialogue with Russia, sought to weaken punishments for corruption and dismantled a special prosecutor's office dealing with high corruption, and proposing to revamp the RTVS public broadcaster despite calls to protect media freedom.
Fico has long been critical of Slovakia's mainstream media, refusing to speak to some outlets. Members of his party blasted media and opposition actions in recent months.
In Germany, which has recently seen a spate of attacks on politicians, Chancellor Olaf Scholz expressed shock on Wednesday, saying that violence had no place in European politics.
