"It is about time that member states stepped up to the plate and did what they need to do," European Commission Vice-President Frans Timmermans said as EU leaders gathered in Brussels for an emergency summit on the migrant crisis.
"A common asylum system can only work if every country respects the rules," Timmermans said after officials met to prepare for the summit.
The 28-nation EU has established a whole series of rules governing the handling of asylum seekers in Europe, from their arrival, to registration, treatment and rights pending a decision.
EU interior ministers agreed yesterday to relocate some 120,000 processed asylum seekers around the bloc but this is an emergency measure and falls outside the new system.
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Timmermans said the Commission, the EU's executive arm, had taken the first step in 40 infringement procedures, in addition to 35 already opened, by sending formal letters of notice to the concerned countries.
This was not only necessary in terms of dealing with the influx of refugees but was also an essential step to ensuring the EU's passport-free Schengen zone could work properly.
Several member states, especially in eastern Europe, have closed their borders or suspended crossing points in an attempt to halt the refugee influx, in violation of Schengen rules.
Timmermans said that if the rules were properly applied, "this would be one way to restore confidence in the Schengen area."
Greece, Italy and Hungary, which have borne the brunt of the migrant inflow, are also on the list.