The top Czech diplomat wrote in the Financial Times that Britain's exit negotiations and EU reforms must be approached with humility and that acting too quickly would be dangerous.
He said it would be dishonest to pin all the blame for the British vote on the country's politicians and voters, calling the Brexit "a symptom of a wider crisis of trust and the collapse of the EU's political capital."
"The (EU) bodies that are meant to instil a sense of common purpose have become symbols of alienation," Zaoralek wrote in a FT commentary that his ministry posted on its website.
"Instead of protecting the unity of the EU, they have contributed to national division and public mistrust, especially in their response to the refugee crisis."
The Commission has irked the central and eastern EU states with efforts to impose fixed quotas on taking in some of the 1.3 million refugees and migrants who reached Europe last year.
The central European countries of Poland, Slovakia, Hungary and the Czech Republic called this week for more powers to be repatriated from Brussels to EU capitals and for a reduction in the role of the Commission, with many politicians critical of its integrationist chief, Jean-Claude Juncker.
On Thursday, Slovak Prime Minister Robert Fico said states like his that joined the bloc after 2004 need to have more involvement in the EU's future as this could not be decided by just two or three powerful Western members.
Zaoralek said he was "truly baffled" by proposals for further EU integration in the wake of the British vote. "The only thing more dangerous than a federalist push would be moves by member states to reclaim national sovereignty," he wrote.
Zaoralek called evolution toward a more diversified EU a fact of life. He said his country wanted to be a core part of it if the process remains inclusive and added that EU institutions should have a leading role in the process.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)