The suspension of free movement measures along Germany's 800 km border with Austria prompted media speculation over the future of the EU's internal border control rules.
The Guardian's Brussels correspondent, Ian Traynor, called Berlin's decision to shut its main entry point to asylum seekers flowing in from the war torn regions in Syria, Iraq, Afghanistan and Eritrea in East Africa a "telling blow to two decades of open travel" for the EU's so-called Schengen agreement.
The agreement, first ratified in 1985, eliminates border checks among its members and allows foreign visitors to travel throughout the Schengen area using one visa. However, several EU countries, including the UK and Ireland, maintain opt-outs to the scheme and manage their borders independently.
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However, European Commission President Jean-Claude Juncker moved swiftly to dampen speculation on the demise of Schengen, also saying on Sunday that Germany's move, reversing its earlier policy of waiving EU asylum policy rules, was both temporary and legal.
In a short statement the commission said, "President Jean-Claude Juncker this afternoon (Sunday) spoke on the phone with Chancellor Angela Merkel where she informed him about the temporary reintroduction of controls at the borders with other EU member states, particularly at the German-Austrian border."
"The temporary reintroduction of border controls between member states is an exceptional possibility explicitly foreseen in and regulated by the Schengen borders code, in case of a crisis situation."
"The current situation in Germany, prima facie, appears to be a situation covered by the rules."
However, Juncker warned that the Commission would be closely monitoring the situation, with the aim of reopening the German-Austrian border, "between Schengen member states as soon as feasible".
He also highlighted that Germany's border shutdown following a surge of around half a million people into the country, "underlines the urgency to agree on the measures proposed by the European Commission in order to manage the refugee crisis."
He added that the German decision was another reason why today's (Monday) extraordinary meeting of EU interior ministers "is so important."
"We need swift progress on the Commission's proposals [on the relocation of asylum seekers] now."