Slovakia‘s interior ministry confirmed it was an assassination attempt.
Mr Fico, 59, was conscious when he was flown to hospital, a spokesperson said.
He was taken to a facility in Banska Bystrica, closer to the scene, as it would have taken too long to get to Bratislava.
“The next few hours will decide,” said a post on Mr Fico’s Facebook page.
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0:18
Slovakian PM bundled into car after being shot
Two people who saw the attack told local news outlet Diary N about the moment it 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.
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3:33
Who is Robert Fico?
Robert Fico: A divisive figure sympathetic to Putin
Robert Fico is a populist who staged a political comeback last year.
The 59-year-old has previously been compared to former US president Donald Trump.
But his election victory last autumn meant NATO also had its first leader who was sympathetic to Russia’s Vladimir Putin.
Critics have voiced increasing fears Mr Fico would abandon Slovakia’s pro-Western course.
This would follow the direction of Hungary’s prime minister, Viktor Orban.
Thousands of people have repeatedly held protests across Slovakia against his policies.
Mr Fico and his SMER, or Direction, party secured nearly 23% of the votes at the polls in October.
He is known for foul-mouthed tirades against journalists and has campaigned against immigration and LGBTQ+ rights.
The prime minister has previously opposed EU sanctions on Russia – and has been against Ukraine joining NATO.
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 needed protection.
The politician founded the SMER party in 1999 and has served as the nation’s prime minister for over 10 years across three different spells.
With a campaign based on overturning austerity reforms, Mr Fico started his first four-year spell as the country’s leader in 2006.
He returned as leader in the parliamentary elections of 2012, but failed in an attempt to win the presidential election of 2014.
In 2016, despite winning the parliamentary polls, Mr Fico’s party was unable to secure a majority and after a multi-party coalition allowed him to remain as leader, he resigned in 2018.
Slovakia’s president, Zuzana Caputova, called it a “brutal and ruthless” act – and leaders from across Europe have condemned the assassination attempt.
European Commission chief Ursula von der Leyen called it a “vile attack”, while Czech leader Petr Fiala said it was “shocking”.
Polish Prime Minister Donald Tusk posted on X: “Shocking news from Slovakia. Robert, my thoughts are with you in this very difficult moment.”
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