Slovakia‘s interior minister said there was a “clear political motivation” behind the attack, while local TV said Mr Fico was hit in the stomach.
The 59-year-old was taken to a local hospital and then flown to a larger facility in Banska Bystrica.
“The next few hours will decide,” said a post on Mr Fico’s Facebook page.
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Slovak PM bundled into car
The prime minister was still in surgery on Wednesday evening, said the country’s defence minister, who described his condition as “extraordinarily serious”.
Interior minister Matus Sutaj-Estok told reporters outside the hospital that the gunman had fired five shots.
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Two witnesses told local news outlet Diary N about the moment the shooting happened.
“I was just going to shake his hand,” said one.
“When the shots rang out, I almost became deaf,” said the other, who did not want to give her name.
She said there were three or four shots and that Mr Fico fell to the floor with blood on his chest and head.
Other witnesses said the gunman used a friendly nickname to call out to the prime minister as he approached a crowd of supporters.
Slovak media said he was a former security guard and an author of poetry collections.
‘A polarising political bruiser’
By Darren McCaffrey, political correspondent
Robert Fico has been in Slovak politics for decades, even before the country of Slovakia existed.
A towering figure, he is a political bruiser who has been polarising at home and throughout Europe.
His election last year seemed almost unimaginable until recently, after Fico was forced to resign following the murder of a famous journalist and allegations of corruption.
It appeared his political career was over.
However, he bounced back on a campaign to end military support for Ukraine.
He is also resistant to sanctions on Russia, a conservative on social issues and he attacks the EU project.
This populist approach has a large constituency with mainly rural, older, conservative voters helping him to a third term.
But not with everyone, his party did receive the largest number of votes, though it only amounted to 23%.
Slovakia, like many of its neighbours, is deeply divided with younger, more metropolitan voters angry with the nationalistic approach to politics.
They tend to be more pro-EU, in favour of Ukrainian support and liberal.
There is also widespread concern about an authoritarian approach to politics, curbing of media freedoms and opposition parties.
The result is a polarised country with a polarising prime minister who has never shown any sign of wanting reconciliation.
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Who is Robert Fico?
Robert Fico on the world stage
Robert Fico’s election victory last autumn meant NATO had another leader – alongside Hungary’s Victor Orban – who is sympathetic to Russia’s Vladimir Putin.
He has previously opposed EU sanctions on Russia – and has been against Ukraine joining the defence treaty.
He believes the US and other nations should use their influence to force Russia and Ukraine to strike a compromise peace deal.
Mr Fico also repeated Mr Putin’s unsupported claim that the Ukrainian government runs a Nazi state from which ethnic Russians in the country need protection.
Critics have also voiced increasing fears Mr Fico would abandon Slovakia’s pro-Western course.
World leaders – including Vladimir Putin and Joe Biden – have been quick to condemn the shooting.
European Commission chief Ursula von der Leyen called it a “vile attack”, while Czech Prime Minister Petr Fiala said it was “shocking”.
“News of the cowardly assassination attempt on Slovakian Prime Minister Fico shocks me deeply,” said German leader Olaf Scholz.
“Violence must have no place in European politics.”
Polish Prime Minister Donald Tusk posted on X: “Shocking news from Slovakia. Robert, my thoughts are with you in this very difficult moment.”
Mr Fico is a three-time premier in Slovakia and a stalwart of the country’s political scene.
However, he is a divisive figure, with many critical of his more sympathetic stance towards Russian President Vladimir Putin and views on LGBTQ rights.
He won elections in September after campaigning on a pro-Russian and anti-American message.
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