The move shows the frustration in Brussels over the slow response to the scheme, which aimed to relocate 160,000 migrants from frontline migrant crisis states Italy and Greece but which has so far seen only 20,000 moved.
"I regret to say that despite our repeated calls, the Czech Republic, Hungary and Poland have not yet taken the necessary action," EU Migration Commissioner Dimitris Avramopoulos told a news conference.
"For this reason the (European) Commission has decided to launch infringement procedures against these three member states," he said at the European Parliament in Strasbourg, France.
Brussels last month set a June deadline for Warsaw and Budapest to start accepting migrants under the plan to ease the burden on Italy and Greece, or risk sanctions. Prague also came under pressure after effectively dropping out.
'Illegal decision'
The three eastern European states all reacted defiantly to the decision after having led resistance to the plan since its outset in 2015 at the height of the migration crisis, when more than one million refugees landed on Europe's shores.
Czech Prime Minister Bohuslav Sobotka said his government had been active on the crisis but tweeted: "Quotas are not working."
Poland's Foreign Minister Witold Waszczykowski hit out at the "illegal decision", insisting that most of those being relocated were migrants who should be sent home and not refugees needing international protection.
Hungarian Foreign Minister Peter Szijjarto said his government would "not give in to blackmail".
Brussels is already at odds with Budapest over rights issues, including a crackdown on foreign-backed civil society groups approved by the Hungarian parliament on Tuesday.
Avramopoulos, who is Greece's European commissioner, insisted those selected for the relocation scheme had all been carefully screened and identified as needing international protection.
He also criticised the three countries for expecting the benefits of EU membership while not taking on responsibilities.
"Europe is not only about requesting funds or ensuring security," Avramopoulos said. "Europe is also about sharing difficult moments and challenges and common dramas."
UN refugee chief Filippo Grandi expressed "disappointment" that the lion's share of protecting refugees on such a wealthy continent should fall on so few countries, such as Italy, Greece, Germany and Sweden.
Amnesty International hailed the EU decision, with the rights group's European head Iverna McGowan saying it "makes it clear that countries will not be allowed to get away with dragging their feet to avoid accepting refugees."
Stiff penalties
Under "infringement" proceedings the European Commission, the 28-nation EU's executive arm, sends a letter to national governments demanding legal explanations over certain issues, before possibly referring them to the European Court of Justice.
EU states can eventually face stiff financial penalties if they fail to comply.
Avramopoulos said Hungary and Poland were targeted because they had failed to admit one single person under the plan to redistribute among other member states 160,000 mainly Syrian, Eritrean and Iraq asylum seekers from Greece and Italy by September.
He said the Czech Republic was targeted for having relocated nobody in the past year and failed to issue any new pledges to admit asylum seekers.
Hungary, the Czech Republic, Slovakia and Romania opposed the scheme two years ago but were overruled by a majority vote that is legally binding. Poland reluctantly agreed to the plan but took an even harder line when a new right-wing government assumed power weeks later.
Hungary and Slovakia have since taken their case to the EU's top court.
In the latest EU figures, just over 20,000 people have been relocated under the plan, which was in response to Europe's biggest ever migration crisis.
European sources have blamed the delays on a series of factors: governments trying to screen jihadists in the wake of terror attacks, a lack of housing and education for asylum seekers, and logistical problems.
They said some countries were setting unacceptable conditions by refusing Muslims, black people or large families, with Eastern European states the worst for discriminating on religious or racial grounds.
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