Czech Prime Minister Andrej Babis has lost a confidence vote in parliament, an expected result that marks the end of his short-lived minority government.

Only 78 members of parliament on Tuesday voted in favour of the government, while 117 were against.

Babis, the country's second-richest man, and his cabinet will hand in their resignation on Wednesday, a spokeswoman said.

However, the prime minister is expected to remain in office as he negotiates with opposition parties to form a new government.

Babis' ANO movement won October's parliamentary elections, with 78 seats in the 200-seat house. His government of ANO members and independent experts was appointed last month.

Czech President Milos Zeman, who is tasked with appointing prime ministers, has said he is willing to give Babis a second chance.

{articleGUID}

However, Zeman is up for re-election himself in a runoff that will be held on January 26-27.

It is unclear if Babis will get that second chance if Zeman loses to his opponent, Jiri Drahos.

Opposition parties have said they are ready to talk about joining a coalition, with some of them only willing to come to the table if Babis was not prime minister.

"The ANO chairman should wake up from his dream about a minority, one-party government and he should start working normally, work on building a government with majority support in parliament," Petr Fiala, head of the centre-right Civic Democrats said.

That demand mainly sprouted from fraud allegations against Babis.

He is alleged to have hidden ownership of one of his companies a decade ago to win a $2.45m subsidy, mostly from European Union funds, meant for small businesses.

Babis, the second richest man in the Czech Republic, has denied any wrongdoing, saying the investigation is a ploy to try to get him to leave politics.

{articleGUID}

"This is a ploy organised by the mafia that had been stealing billions here, for a long time, and I, of course, bother them," Babis said on Tuesday.

After winning the October elections, Babis regained previously revoked immunity from prosecution.

However, Czech police have requested Babis' immunity to be lifted, a course of action a parliamentary committee also recommended earlier on Tuesday.

With parliament giving a vote of no-confidence and presidential elections happening next week, it could take weeks - if not months - before the Czech Republic has a government.