The announcement came as tragedy struck again off the coast of Greece, with 34 more migrants -- among them babies and children -- drowning when their overcrowded wooden boat capsized in high winds.
German Interior Minister Thomas de Maiziere said border controls would be reintroduced with immediate effect, and the Czech republic announced similar measures on the border with Austria.
"The aim of this measure is to stop the current influx to Germany and to return to an orderly process," de Maiziere said, as the city of Munich recorded an influx of 63,000 asylum seekers in two weeks.
Under EU rules, the first country of entry is required to deal with an asylum-seeker's request for protection, but Germany had waived the rule for Syrian refugees.
Local authorities in Germany, which has earned praise for its welcoming stance towards refugees, have buckled under the sudden surge of migrants at the end of an exhausting and often perilous journey.
European Union home affairs ministers will hold an emergency meeting tomorrow to discuss deeply divisive European Commission plans to introduce compulsory quotas for refugees.
"The German decision of today underlines the urgency to agree on the measures proposed by the European Commission in order to manage the refugee crisis," the EU said.
"Given the numbers from yesterday, it is very clear that we have reached the upper limit of our capacity," said a Munich police spokesman.
In Greece, on the frontline of the massive surge of people trying to reach Europe, the coastguard said 34 people -- including four babies and 11 young children -- perished when when their boat capsized off the Aegean island of Farmakonisi.
The coastguard was also still searching for four children missing after another boat capsized yesterday off Samos, a Greek island just off the Turkish coast.
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