State election officials citing results from nearly 73 per cent of polling stations said Babis's anti-corruption and anti-euro ANO (Yes) movement was ahead with 30.87 per cent support with the far-right Freedom and Free Democracy (SPD) in second place on 11.19 per cent.
The eurosceptic right-wing ODS party has clinched third spot with 10.51 per cent and the anti-establishment Pirates scored 10.04 per cent.
Far-right and far-left anti-EU parties made gains in a fragmented vote that appeared to put eight parties into the 200-seat Czech parliament with few natural coalition allies among them, something analysts warn could herald instability and even chaos.
The Social Democrats (CSSD) who head the outgoing coalition government took a bruising, coming in sixth with 7.67 per cent of the vote.
Voting earlier today, outgoing Social Democrats (CSSD) Prime Minister Sobotka warned the election "will decide about our country's focus, whether we stay part of the EU and NATO, or whether extremist forces trying to drive us out of these structures will post gains."
France's far-right National Front Marine Le Pen sent Okamura a message of support.
"I see this as a threat to liberal democracy" in this EU member of 10.6 million people, Tomas Lebeda, a political analyst at Palacky University in the central city of Olomouc, told AFP.
"The SPD is a clearly an anti-system, populist party. It seems this type of party will score its best-ever result in Czech history," he said, but added that the SPD was unlikely to enter the future government
"In the four years since the last election, pensions have gone up, just like wages and welfare benefits," he told AFP.
With joblessness at 3.8 per cent in September, the Czech economy which is heavily reliant on car exports is slated to grow by a healthy 3.6 per cent this year.
But other voters did not conceal their disillusionment.
Young Prague voter Jiri Chaloupek said he chose the SPD as "this country needs a change, a rather radical change."
"I'm asking myself what the elections would look like if we weren't in such good shape economically."
A 63-year-old Slovak-born chemicals, food and media tycoon, Babis said he expected the Czech Republic to "enter a new stage" after voting on Friday, adding it needed "a government which will really tackle people's problems.
While the billionaire-politician has vowed to steer clear of the eurozone and echoes other eastern EU leaders who accuse Brussels of attempting to limit national sovereignty by imposing rules like migrant quotas, he favours a united Europe and balks at talk of a "Czexit".
Babis's main rival, Social Democrats leader and Foreign Minister Lubomir Zaoralek has said he hoped that the future government would ensure that the Czech Republic does not drift to the EU's periphery.
Partial results showed the anti-EU Communists took fifth spot winning 8.51 per cent support.
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