Opinion surveys show the divisive 73-year-old ex- communist, who is also staunchly anti-Muslim and pro-Chinese, leading the pack of nine candidates ahead of Jiri Drahos, 68- year-old pro-European former head of the Czech Academy of Sciences.
Although Zeman is in pole position as the country kicks off a final day of first-round voting today, the outspoken head of state is unlikely to win an outright majority. A run- off vote is expected on January 26-27.
The topless protester from Ukraine's Femen group was overpowered by bodyguards and then arrested by police.
Security personnel also had to help a visibly rattled Zeman, who walks with a cane, to leave the room.
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Prague voter Martin Sauta said he voted for Zeman as he has "the most consistent views", while his rivals are "completely shapeless".
But Prague wine bar owner Eva Simova, 53, told AFP that he was voting for Drahos: "He seems like an honest guy and what's more, I'm sick and tired of Zeman."
Zeman's rhetoric echoes populist-minded eastern EU leaders -- especially in Hungary and Poland -- at odds with Brussels over mandatory refugee quotas and various rules they see as attempts to limit national sovereignty.
He is also stridently anti-Muslim, having once called the 2015 migrant crisis "an organised invasion" of Europe and insisted Muslims were "impossible to integrate".
The country of 10.6 million people has received only 12 migrants under the EU quota system.
Drahos could not be more different. A mild-mannered liberal centrist whom critics have dubbed "wishy-washy", he has called for Prague to "play a more active role in the EU" and has backed the adoption of the euro currency.
"The president should work to unite society. It's clear that not everyone can agree, but the current president doesn't unite people, he divides them," Drahos added.
Independent analyst Jiri Pehe said the vote highlights a "polarised" society.
"It is a clash between... the post-communist part of society represented by Zeman and the other part, say, modern, pro-Western, which simply doesn't want this president any more," he told AFP.
Zeman has the backing of embattled billionaire Prime Minister Andrej Babis, who said the incumbent "fights for our national interests" but called on him to "unite, not divide" Czechs.
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.
Pehe said a victory for Zeman might "pave the way for a deeper alliance with Andrej Babis, which could lead to a change in some basic parameters of liberal democracy in the country."
But the situation could change dramatically if Drahos wins.
Zeman's other rivals include ex-gambler and songwriter Michal Horacek, and former right-wing premier Mirek Topolanek.
The CTK news agency pegged turnout at 40 per cent after day one of voting.
Polling stations reopen at 0700 GMT today before closing at 1300.
Soon after that initial results will indicate which two candidates are likely to contest the expected run-off vote.
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