Border slowdowns and closures along the migrant route through Europe have just meant that people are now piling up in Greece, overwhelming the country's resources, Merkel said at a joint news conference with French President Francois Hollande in Paris.
The two leaders met ahead of a summit of EU and Turkish leaders to discuss the migrant crisis Monday. The Balkan countries and Austria have recently introduced tight restrictions to stem the flow of migrants. That has resulted in thousands of refugees and other migrants being stranded by Greece's border with Macedonia.
Germany and France agree that the EU has to protect its external border to preserve freedom within Europe, get away from internal border controls and for security reasons, Merkel said.
Hollande said France will provide a ship to the NATO force deployed in the Aegean Sea between Turkey and Greece to help Europe's external border control.
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As temporary controls between several member states are reimposed to deal with the migrant crisis, some fear a full collapse of the borderless Schengen zone through most of the EU.
More than 1.2 million people applied for asylum for the first time in the EU last year, more than double the number in 2014.
The EU's statistics agency said today that most people applying in the 28 EU countries were Syrian, Iraqi or Afghan nationals. It said 362,800 Syrians applied for asylum.
The bloc today kicked off the distribution of the promised USD 3.3 billion in aid for refugees in Turkey, formally pledging 95 million euros for educational and food assistance.