Berlin announced that the temporary measure would be taken first on the southern frontier with Austria where refugee arrivals have soared
Germany re-imposed border controls on Sunday after Europe's most powerful nation acknowledged it could scarcely cope with thousands of asylum seekers arriving every day.
A day before deeply divided European Union ministers tackle the refugee 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 refugee 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 Monday, 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 Sunday 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 Sunday 34 refugees, almost half of them babies and children, drowned off a Greek island when their boat sank, the coast guard said.
Germany, Europe's largest and richest economy, has become a magnet for refugees making journeys by sea and land, often via Turkey and the Greek islands, and then onwards through the Balkans, Hungary and Austria. Police said around 13,000 arrived in the southern German city of Munich alone on Saturday, and another 3,000 on Sunday morning.
Now Germany has joined smaller and poorer countries such as Greece and Hungary that are struggling to manage the huge flow of desperate people.
As trains for Germany were stopped, groups of refugees and refugees camped out in an underground carpark in the Austrian city of Salzburg, near the border. Traffic backed up along one of the highways between the two countries.
Austrian news agency APA quoted Chancellor Werner Faymann as saying that Vienna would not introduce additional border controls for now but that the effect of Germany's decision on Austria was hard to predict.
Trains from Austria to Germany would be stopped until 5:00 a.m. (0300 GMT) on Monday, the interior minister of the state of Bavaria said. A Reuters photographer also saw a German police checkpoint on one of the Austrian roads into Germany.
German police on the border with Austria said they had detained 22 smugglers since Berlin implemented border controls. Forty-four refugees also were rounded up and taken by bus to registration centres, a police spokesman said.
Germany made clear it wanted EU partners to share the burden of welcoming thousands of refugees.
"It's true: the European lack of action in the refugee crisis is now pushing even Germany to the limit of its ability," Economy Minister Sigmar Gabriel, who is also vice-chancellor, told the website of Der Tagesspiegel newspaper.
With large numbers of refugees stuck in squalid and chaotic conditions on European borders, or trudging along the side of motorways, Merkel last weekend stopped enforcing the EU's "Dublin" rules under which asylum seekers should register in whichever member state they first arrive in.
De Maiziere defended Merkel's decision but insisted the Dublin rules were still valid. "We need to quickly return to orderly procedures now," he added. "We can't allow refugees to freely choose where they want to stay - that's not the case anywhere in the world."
Most asylum seekers are refusing to stay in the poorer southern European countries where they arrive, such as Greece, and are instead making their way to Germany or Sweden where they anticipate a warmer welcome. Many Germans have greeted the arrivals with cheers and volunteers are flooding in to help.
"We are helping, we are ready to help, but on a voluntary basis," Czech Prime Minister Bohuslav Sobotka said on Sunday. "The quotas won’t work."
In neighboring Slovakia, Interior Minister Robert Kalinak said he would try to block quotas. "They don't make any sense ... and don't solve the crisis in any way," he said in a TV interview.
Poland said it might accept more refugees, but only if the EU secures its external borders; separates those who need help from economic refugees; and allows Warsaw a say in screening them from the point of security.
Meanwhile, the refugees continued to risk all on their journeys. The Greek coastguard said the 34 drowned off the island of Farmakonisi, almost certainly the largest death toll in those waters since the refugee crisis began.
In the space of 90 minutes, a Reuters photographer saw 10 dinghies packed with refugees arriving from Turkey on the Greek island of Lesbos.
Further up the refugee route, 8,500 refugees entered Macedonia from Greece between Saturday evening and Sunday afternoon, the UNHCR said.
Hungarian state TV M1 reported that 8,000 to 10,000 refugees had crossed into Austria at Hegyeshalom by 6 pm and several thousand more were expected by the end of the day.