The vote, likely to end in a run-off in two weeks’ time, is seen as a referendum on the 73-year-old Zeman, in office since 2013, who has criticised migration from Muslim countries and Germany’s decision to accept many migrants in Europe.
Early results show Zeman has taken 39 per cent of the vote against eight competitors, with his closest rival Jiri Drahos, 68, taking 24.2 percent. Drakes is likely to go head to head with Zeman in the second run off if the results remain the same.
So far, 90 percent of the vote has been counted.
Polling stations closed at 2 pm local time (1300 GMT) and results are expected this evening.
Czech presidents have limited executive powers but Mr Zeman and his predecessors have had a strong influence on public debate. They are also pivotal in forming governments – which the European Union and NATO member country is now trying to do.
A win by any of Mr Zeman’s main rivals could mean that voices from the Czech leadership may shift closer to the EU mainstream.
A former centre-left prime minister and backer of a federal Europe, Mr Zeman has gradually shifted to positions criticising the EU, echoing and reinforcing public sentiment.
He has won endorsements from some mainstream groups as well as the Communist Party and the main far-right anti-EU and anti-NATO SPD party.
The Czech Republic has a tiny Muslim minority and has seen few of the hundreds of thousands of people coming to Europe in the past years to seek safety from war or better life. Like Slovakia and Hungary, the Czechs have clashed with the European Commission over their refusal to accept migrants under quotas set by a vote by EU leaders.
Mr Zeman has sought more trade and closer ties with China and has warm relations with Russian President Vladimir Putin, calling for the removal of EU sanctions on Russia over its annexation of Ukraine’s Crimea to boost business.
Public opinion, the most eurosceptic in the EU, may also be affected by a change of tone from the top.
“I voted for professor Drahos because I want that someone who will not push us to the East and who will not be a disgrace,” said lawyer Matej Gredl, 30, after he voted in Prague.
Earlier on Saturday John Simpson a BBC reporter, told the Today programme that “Eurocrats in Brussels” are praying that the incumbent Milos Zemen “does very badly”.
Mr Simpson said: “The French, the Germans, the Eurocrats in Brusels are praying today that President Zemen does badly.
“In reality both Zemen and Drahos will do quite well, but not enough to win outright.”
Since Brexit Brussels has been claiming there is a strong feeling of unity among the remaining 27 member states yet the Visegrad Group, Czech Republic alongside Hungary, Poland and Slovakia say differently.
Each of the states has rallied against the EU and rulings made in high courts.
Hungary is to be taken to court over its refusal to take part in migrant quotas while Poland has also been accused of breaking Eu rules.
Since no candidate won more than 50 percent, the two contenders with the highest number of votes will face each other in a run-off round on January 26-27.
Milos Zeman 39.24
Jiri Drahos 26.26
Pavel Fischer 10.07
Michal Horacek 9.09
Marek Hilser 8.80
Mirek Topolanek 4.22
Jiri Hynek 1.23
Petr Hannig 0.57
Vratislav Kulhanek 0.48