The opposition failed to reach the 101 votes needed in the 200-member parliament to topple the cabinet, with 85 lawmakers voting no confidence in the cabinet, and 85 voting against.
Billionaire Czech Prime Minister Andrej Babis survived a no-confidence vote early on Thursday, even as he faces charges of graft, EU concerns over possible conflicts of interest and mass rallies demanding his resignation.
The opposition failed to reach the 101 votes needed in the 200-member parliament to topple the cabinet.
"Eighty-five lawmakers voted no confidence in the cabinet, and eighty-five voted against," said Jana Cernochova, a lawmaker in charge of the vote, after a marathon 17-hour session.
Only 170 lawmakers voted, with the remaining 30 either absent or ab staining from voting.
Babis's ANO movement leads a minority coalition with the Social Democrats (CSSD), relying on informal backing from the Communists for a majority of 108 seats in the parliament.
The CSSD voted in favour of the cabinet and the Communists abstained.
The 64-year-old Slovak-born Babis, who made his fortune as the founder and owner of the sprawling Agrofert food, chemicals and media holding, has come under fire over murky business dealings.
He faces police charges in connection with a $2.25 million (two million euro ) EU subsidy scam, while the EU is probing his dual role as politician and entrepreneur.
Babis allegedly served as a Communist secret police agent in the 1980s when the former Czechoslovakia was behind the Iron Curtain.
Babis staunchly denies any wrongdoing, insisting that the EU audit contained "errors" and characterising the other allegations as a smear campaign.
"The vote is not as much about the government as it is about me," Babis told lawmakers on Wednesday as the session began.
"I don't really understand. This is an attempt to destabilise our country, it's against the interests of our citizen s," he added.
"I am the prime minister of all Czech citizens, I fight to defend their interests... I don't know who can blame me for anything," he said, adding that he hoped the cabinet would complete its four-year mandate.
Babis has been the target of massive rallies since the appointment in April of Justice Minister Marie Benesova, seen as an ally who could sweep the charges against the PM under the rug.
More than 250,000 people rallied in Prague on Sunday demanding that Babis resign in the biggest Czech protest since the fall of Communism in 1989.
Despite the upr oar, ANO – described by critics as a one-man party – tops opinion polls with 30 percent support and won May's European Parliament elections.