In doing so, the court ignored the advice of Eleanor Sharpston, its British advocate-general, who warned that the system could leave border states “unable to cope”.
The court ruled on the cases of two Afghan sisters and a Syrian man who entered the EU during the 2015 crisis.
The Jafari sisters, Khadija and Zainab, entered the EU through Croatia after fleeing Afghanistan with their children. At the time, Mrs Merkel had opened Germany’s borders to migrants and Austria was operating a similar policy.
Croatia allowed the sisters and their children to cross its territory in order to reach one of the two countries.
They claimed asylum in Austria, but the Austrian government later reversed its position and returned the families to Croatia, ordering them to seek asylum there.
The sisters challenged the decision, arguing they should be given asylum in Austria as they had been allowed to cross Croatia and had not entered its territory illegally.
In a second case, an unnamed Syrian man challenged his deportation from Slovenia to Croatia under similar circumstances.
The court rejected the challenges, ruling that the fact Croatia had allowed the migrants to cross its territory did not mean the Dublin rules had been waived.
The ruling will be welcomed in central European countries like Austria and Slovenia, where there is considerable political resistance to letting in more migrants.
But it will cause concern in the countries where most migrants first enter the EU, Italy and Greece, which complain the system leaves them to shoulder too much of the burden.
The court’s decision was unexpected, after the judges took the unusual step of ignoring the advice of the advocate-general.
In a written opinion issued last month, Ms Sharpston warned that the Dublin system “was simply not designed to cover such exceptional circumstances”.
“If border member states, such as Croatia, are deemed to be responsible for accepting and processing exceptionally high numbers of asylum-seekers, there is a real risk that they will simply be unable to cope with the situation,” she wrote.
While the ruling will be seen as a victory by many in central Europe, Hungary and Slovakia suffered a setback in a separate case over EU quotas for sharing asylum-seekers between member states.
In an opinion presented to the court, Yves Bot, another advocate-general, said the court should reject a bid by the two countries to have the quota system overturned.
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