Andrej Babis railed against the EU for not taking into account the opposition to policies such as the quotas, which Prague and other Central European capitals have rejected.
A controversial relocation system for mainly Syrian refugees – introduced in 2015 – shared out 120,000 asylum seekers from Greece and Italy in summer of the same year – with Hungary taking no action to pledge their relocation.
Eastern-European states have seen a larger rise of Euroscepticism since the continent’s migration crisis in 2015, sparking long-running battles between far-right populist movements and the bloc.
The Czech Republic, along with Poland and Hungary, is set to be sued by the European commission in the bloc’s European Court of Justice for their refusal to host asylum seekers.
But Mr Babis, a 63-year-old billionaire businessman whose ANO party came first in October’s national parliamentary election, insists he is pro-EU and the best the bloc could hope for, according to Politico.
Asked if he saw himself as a defender of the EU in the Czech Republic, he said “of course”.
He believes he is the EU’s best – and perhaps last – chance to prevent anti-EU radicalisation back home.
He said: “In the Czech Republic, we have some extremist parties, who would like a ‘Czexit’.
“They are in parliament and got 11 percent [in the October election].
“What we need is an understanding of our political situation, because the next time maybe Mr. Okamura will receive 30 percent.”
Echoing a message also made repeatedly by other European countries, Babis said the EU should tackle migration by reinforcing its external borders and offering more aid to the Middle East and Africa.
He said: “These quotas are dividing Europe and are ineffective.
“It’s a problem mainly for the image of Europe in the eyes of our citizens and it’s a pity because of course Europe is an excellent project.”
Despite showcasing his enthusiasm for the bloc, he said the EU could not function if France, Germany and the European Commission did not take account of the views of other member countries.
He said: “We cannot be in a position where we have nothing to say, that there are only two big nations and the Commission that are deciding everything.”
Mr Babis also suggested Euroscepticism could grow in the Czech Republic as a result of cuts to the Common Agricultural Policy.
If Czech farmers were hurt by cuts, he said, it would add to a sense of alienation among voters already angry at an EU directive on firearms possession and the migrant quotas.
He added: “It’s then difficult to explain for our citizens that the EU is a good project.”