However, with nearly all ballots counted by the Czech Statistics Office, Zeman had 38.6 percent of the vote, a commanding lead over Drahos' 26.6 percent.
Jiri Drahos, the former head of the country's Academy of Sciences, was the clear runner-up with 26.56 percent.
During his five-year tenure to date, President Milos Zeman has become known for his plain-speaking nature and tough opposition to Muslim integration.
Zeman was elected in 2013 during the country's first direct presidential vote, a victory that returned the former left-leaning prime minister to power.
Otherwise, the president has little executive power since the country is run by a government chosen and led by the prime minister.
"I assume citizens have their own opinion and their own reason".
Tapped by Zeman for prime minister in December, Babis was forced to form a minority government which appears set to lose a parliamentary confidence vote on January 16.
"I like that he speaks to voters", said Irena Matuskova, a Prague nurse who plans to vote for Zeman.
Zeman has backed Babis even as the billionaire businessman has struggled to get support from other political parties while he battles police allegations he illegally obtained European Union subsidies a decade ago.
The Czech government is led by the prime minister, but unlike other countries where the president has a largely ceremonial role, the Czech president is involved in numerous country's political decisions.
The Czech Republic is a member of a regional alliance of Central European nations called the Visegrad Group, alongside Hungary, Poland and Slovakia.
"Zeman has won backing from poorer and rural voters in the country of 10.6 million by opposing what he calls urban elites detached from the lives of ordinary people", Bloomberg writes. Drahos said he needed to boost his visibility outside the capital - the only region he won - and would focus on that ahead of the second round.
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