German Interior Minister Thomas de Maiziere said Germany had temporarily introduced controls along its border with Austria in an attempt to reduce the number of asylum seekers arriving in the country.
"At this moment Germany is temporarily introducing border controls again along (the EU's) internal borders. The focus will be on the border to Austria at first," he said.
"The aim of these measures is to limit the current inflows to Germany and to return to orderly procedures when people enter the country," he said, adding that this was also necessary for security reasons.
People fleeing war and poverty in Syria and other parts of the Middle East and Africa have streamed into Germany in recent weeks. Police said around 16,000 migrants arrived in Munich between Saturday morning and yesterday afternoon.
De Maiziere said Germany would continue to stick to European and national guidelines on protecting refugees and stressed that Europe's "Dublin rules", which require asylum seekers to apply in the first EU country they reach, continued to be valid.
He urged all EU member states to stick to the "Dublin" rules in future, adding: "That means that the responsible member state does not only register the asylum seekers but also carries out the asylum procedure."
De Maiziere said refugees needed to accept that they could not simply choose an EU member country to protect them and he said this would also be the case if a European system for distributing them across the bloc is introduced.
"This step became necessary. The great willingness to help that Germany has shown in recent weeks, by full-time employees and especially by the many thousands of volunteers, must not be overstrained," he said.
He also said the introduction of border controls, on which Germany consulted with Austria, could restrict traffic and train transport.
Thirty-four refugees, almost half of them babies and children, drowned when their boat sank off a Greek island yesterday, almost certainly the largest death toll in those waters since the migrant crisis began, the coastguard said.
Four babies, six boys and five girls died when the wooden vessel carrying them overturned about three miles (5 km) east of the small island of Farmakonisi, close to Turkey's coast, the service added.
Tens of thousands of mainly Syrian refugees have braved rough seas this year to make the short but precarious journey from Turkey to Greece's eastern islands, mainly in flimsy and overcrowded inflatable dinghies.
Thousands have died, many of them taking the much longer crossing from Libya, in Europe's worst migrant crisis in decades.
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