European Commission President Jean-Claude Juncker urged the Czech Republic on Thursday to reconsider its decision to stop accepting migrants under an EU plan to share asylum seekers who arrived in Greece and Italy.
The central European country only took in 12 people out of its quota of 2,691 under the scheme to relocate 160,000 migrants from the EU's southern fringe.
The government, which faces an election in October with the majority of the electorate opposed to accepting migrants, agreed on Monday to suspend the program entirely.
This puts the Czechs on a collision course with the EU's executive.
"I was very displeased to read in the press that the Czech government is considering to halt relocations entirely," Juncker said in a speech at Prague's Charles University.
"I sincerely hope that, as in so many other cases, European reason, spirit and values will prevail and that the Czech government will reconsider its course so that we do not have to resort to legal infringement procedures, [which] we will do if nothing changes."
The Czech government cited security concerns and the scheme's failure to function properly for its decision.
Poland, Hungary and Slovakia have refused to admit any asylum seekers under the scheme. Slovakia and Hungary have challenged the quotas in an EU court.
The Commission has said it would decide in June on any legal cases against countries failing to take in their share of refugees and other migrants.
Juncker said EU members benefited from solidarity within the bloc and therefore had to show solidarity with others.
"I am trying to understand national sensitivities about this matter. But more than just a principle, solidarity is a state of mind that goes to the very heart of what the EU is about.
Solidarity is also not a one-way street," he said.