The EU is still struggling to meet its targets on relocation refugees and migrants from Greece and Italy.
In September last year, governments agreed to move one hundred and sixty thousand from both countries to other EU nations.
The deal came as more than one million headed to Europe from the Middle East and North Africa.
“Asylum seekers need to know that they cannot relocate theme-selves. And if they do so they will be sent back. Relocation and resettlement should and will be the ways for them to use in order to reach safety,” said Dimitris Avramopoulos, the EU migration commissioner.
Brussels is well short of its promised goal. Just over 8,000 have been relocated to date.
Officials say there will be some exceptions.
“This (system) only applies to certain categories of migrants: Vulnerable applicants and unaccompanied minors will not be returned to Greece,” added Avramopoulos.
Many EU governments, largely from central and eastern Europe, were sceptical, fearing that agreeing a policy at EU level would only anger voters.
Hungary and Poland have not taken any migrants in from Greece and Italy.
The UK, which can opt out of some European asylum policies, decided not to participate in the scheme.
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