On Wednesday, the European Commission suggested introducing changes to the mandatory quota schemes to redirect all refugees arriving to the bloc through the member countries to aid Greece and Italy.
"The past few months have demonstrated that neither quotas nor the transfer of governments' powers to the European Commission fit," Sobotka said after the Polish-Czech intergovernmental meeting in Warsaw, as quoted by the Novinky online newspaper.
"The decision on which the European Commission insists is poor, it will only deepen the existing problems," Poland's Prime Minister Beata Szydlo said.
Last year, EU members states decided to redistribute some 160,000 migrants across the bloc. Hungary, along with Poland, Slovakia and the Czech Republic, strongly opposed the decision.