Mr Zeman, known for his fierce anti-immigration stance, blasted Brussels for its migration guidelines in an interview with the Prague-based Barrandov TV channel.
He also claimed an influx of refugees from Muslim countries posed a threat to European culture.
Mr Zeman said: “If the European Union does not reach the courage to strengthen its external borders, for which it constantly chatters but does nothing, we will have 10 million refugees from Africa in the course of several years.
“The culture of these refugees is not compatible with European culture, which is what immigrants themselves understand.”
The Czech president is a longstanding opponent of accepting refugees and said the EU should provide financial aid to the countries from which the refugees travel.
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He sparked outrage in 2016 when he called for deportation of all economic migrants claiming there was “a strong connection between the wave of migrants and the wave of jihadis”.
His latest comments come against a backdrop of growing anti-immigration sentiments in the Czech Republic where right-wing and Eurosceptic parties led the country’s parliamentary elections last October.
The Czech Republic is not alone in rejecting some EU policies concerning migrants, with Hungary and Poland expressing similar objections.
EU-ordered quotas obliging the bloc’s member-states to accept the Brussels-mandated number of refugees has been the major point of contention and led to a rift between eastern European leaders and their counterparts in countries such as France, Germany and Holland.
In December, together with Hungary and Poland, Prague refused to contribute to the mandatory resettlement quotas amid pressure from the European Commission, with the trio defiantly stating that its ready to fight Brussels in court.
Czech PM Andrej Babis said: “Quotas are nonsense and only encourage the popularity of extremist parties in Europe.”