A day before deeply divided European Union ministers tackle the migrant crisis, the UN refugee agency also called on every member state to take in a share of asylum-seekers under a Brussels plan which some countries are fiercely resisting.
Berlin announced that the temporary measure would be taken first on the southern frontier with Austria, where migrant arrivals have soared since Chancellor Angela Merkel effectively opened German borders to refugees a week ago.
"The aim of these measures is to limit the current inflows to Germany and to return to orderly procedures when people enter the country," said German Interior Minister Thomas de Maiziere.
Open borders among the European countries which signed the Schengen Treaty are a crucial part of the EU project, but controls can be re-introduced, provided they are only temporary.
"The free movement of people under Schengen is a unique symbol of European integration," the EU's executive Commission said in a statement. "However, the other side of the coin is a better joint management of our external borders and more solidarity in coping with the refugee crisis."
At an emergency meeting on September 14, interior ministers from the EU's 28 member states will discuss Commission proposals to redistribute about 160,000 asylum seekers across the bloc.
"We need swift progress on the Commission's proposals now," the Commission said in a statement issued as tens of thousands of people fleeing war and poverty in Syria and other parts of the Middle East, Asia and Africa made their way north.
EU envoys meeting on September 13 evening in Brussels failed to break the deadlock, with some eastern states still refusing to accept binding quotas of refugees. They argue the plan will draw more people to Europe and disrupt their homogeneous societies.
Amid the political bickering among European governments, the crisis claimed yet more lives. On September 13, 34 refugees, almost half of them babies and children, drowned off a Greek island when their boat sank, the coast guard said.