"Despite the disappointment many of us feel... We must realise that this is not the end of the world and it's absolutely not the end of the EU," Bohuslav Sobotka said on Facebook.
"The EU must change fast, not because Britain has left but because the European project needs much stronger support from citizens," he added shortly after Britain voted to leave the EU in a referendum.
"Europe must be more operational, flexible, less bureaucratic and much more perceptive to the diversity that its member states represent," said Sobotka, the head of a centre-left cabinet.
Some politicians in the Czech Republic, a country of 10.5 million people that joined the EU in 2004, took Britain's decision as an opportunity to flag their euroscepticism.
"I congratulate Britons on their free decision," tweeted Petr Mach, European Parliament member and chairman of the right-wing Free Citizens Party which advocates for "Czexit" on its Facebook page.
Sobotka himself warned earlier this year that Britain's decision to leave the EU might trigger a Czexit debate.
Euroscepticism in the Czech Republic got a boost from the migrant crisis with surveys showing a majority of Czechs opposed to accepting refugees and migrants.
