Billionaire Andrej Babis has won a thumping victory in the Czech Republic's parliamentary election, while eurosceptics and an anti-Islam group made strong gains.

State election officials citing results from 99.9 percent of polling stations on Saturday said Babis' anti-corruption and anti-euro ANO (Yes) movement won with 29.7 percent support, almost three times higher than any other party and giving it a chance to rule with just one partner in a coalition.

ANO was followed by the eurosceptic right-wing ODS party on 11.3 percent.

The far-right, anti-EU and anti-Islam SPD party made strong gains, capturing more than 10 percent of the vote, while another protest party, the Pirates, was set to win a number of seats by appealing to unhappy liberal voters.

At just 7.4 percent, the ruling Social Democrats of Prime Minister Bohuslav Sobotka were on course for their worst result since the country peacefully split with Slovakia in 1993.

In all, a record nine parties were set to win seats. Turnout was at 60 percent.

ANO is the first party to break a quarter century of dominance by two mainstream centre-right and centre-left parties, highlighting a shifting political landscape in Europe where a refugee crisis has given rise to protest groups.

The Czech economy has enjoyed rapid growth, a balanced budget and the lowest unemployment in the European Union in the past four years, but the Social Democrats - who led a government with ANO and another partner - were not able to capitalise.

Instead, ANO and other protest groups took advantage of voters' discontent by promising to weed out corruption, fight deeper EU integration and resist Brussels trying to impose quotas for taking in refugees.

Babis - dubbed the "Czech Trump", a reference to the US president - has promised to bring a businessman's touch to government.

The 63-year-old ran a campaign on opposition to refugee immigration and against closer EU integration.

He maintained his popularity despite facing fraud charges and accusations of conflicts of interest related to his businesses.

ANO is likely to first turn to the Social Democrats for a coalition, its deputy chairman Jaroslav Faltynek told reporters.

However, the Social Democrats' acting chairman said the party may move to the opposition.

Complicating any coalition talks are police charges that Babis illegally received a 2 million euro ($2.35m) EU subsidy when he ran his food, agriculture and chemical empire, worth an estimated $4bn, before entering politics.

He has denied wrongdoing, but party leaders before the election said it would be hard to be part of a cabinet that includes Babis facing a fraud investigation.

His holdings, including interests in national newspapers and a radio station, were placed in a trust earlier this year.

Babis' swipes at Brussels play well with eurosceptic Czechs but he also praises EU membership and does not share the relatively illiberal ideology seen in governments in Hungary and Poland.

Czech President Milos Zeman has said he would allow a month for negotiations before calling a new parliament, the trigger for the current administration to depart. By custom, he asks someone to lead talks before appointing a prime minister.

He told online news website parlamentnilisty.cz he would not object to Babis forming a government even while battling police charges. He also said he would have no objections to talks involving SPD or the Communists.