The commission, the EU's executive body, accused the three countries of "non-compliance with their legal obligations on relocation".
The European Commission today chose to refer the Czech Republic, Hungary and Poland to the Court of Justice of the European Union (CJEU) for non-compliance with their legal obligations as EU members on the relocation of refugees, according to a press release.
The Luxembourg-based ECJ could impose heavy fines.
"The European Commission has today made a decision to refer the Czech Republic, Hungary and Poland to the Court of Justice of the EU for non-compliance with their legal obligations on relocation", the commission said in a statement.
These include Greece and Italy, two countries that have been the first port of call for refugees and migrants, as well as Germany and other wealthy Western nations that are frequently their preferred final destinations.
While most of the member states had relocated the migrants, the Czech Republic, Hungary and Poland had failed to apply the measures fully.
On June 15, 2017, the Commission launched infringement procedures against the three countries on the issue of refugee relocation, taking the process to the next level by sending its "reasoned opinions" on July 26, after the replies provided by the three Member States were found to be unsatisfactory.
He said the quota system had fuelled anti-migrant sentiment and played into the hands of the far right.
The EC's deputy chair Frans Timmermans said a change of attitude on the part of these countries' governments could still resolve the situation out of court.
European Union nations agreed in September 2015 to relocate 160,000 refugees from Italy and Greece as the countries buckled under the arrival of hundreds of thousands of migrants that year.
The move underscores the EU's toughening stance toward both the government of Hungarian Prime Minister Viktor Orban and his right-wing allies in Poland over the bloc's democracy norms and migration.
Budapest also faces legal action over university law.