Croatia has warned it cannot cope with a flood of refugees seeking a new route into northern Europe after Hungary put up a razor wire fence to keep them out.
European Union (EU) leaders are to hold an emergency summit next week to discuss the crisis.
The authorities say at least 11,000 migrants have entered Croatia in two days in the 48 hours since Hungary sealed its southern frontier with Serbia, blocking the previous route to the EU.
Croatia has asked the army to be ready to protect its borders.
At the eastern border town of Tovarnik, riot police struggled to keep crowds of men, women and children back from rail tracks after long queues formed in baking heat for buses bound for reception centres elsewhere in Croatia.
Hungary's closure of its southern border with Serbia has shifted pressure onto Croatia, Slovenia and Romania. People have flooded in since Wednesday's clashes between Hungarian riot police and stone-throwing refugees at the Serbian frontier.
Croatia said it might try to seal its border, but in the meantime it aims to register all new arrivals.
The interior minister, Ranko Ostojic, said those already there must apply for asylum in Croatia or be treated as illegal immigrants.
Meanwhile, Slovenian police have a halted a train carrying 200 migrants and refugees at a railway station on its side of the border with Croatia. They said they would be returned to Croatia "in the shortest time possible".
The Slovenian government said it would not allow illegal migrants to pass through Slovenia, but it would enable them to ask for asylum.
Meanwhile, the Hungarians say about 200 migrants have been detained after crossing into the south of the country from Croatia. There is no fence on that part of the border but Budapest now plans to build one.
The European Union has called an emergency meeting to try to overcome disarray as Europe faces its worst refugee crisis since the Yugoslav wars of the 1990s.
The EU is split over how to handle the influx of hundreds of thousands of people mostly fleeing war and poverty in Syria, Iraq, Afghanistan and Pakistan.
European Council President Donald Tusk has summoned EU leaders to an extraordinary summit next week to discuss migration and a proposed scheme to restribute 120,000 asylum seekers across the bloc.
This week Germany's interior minister, Thomas de Maiziere, said refugees could "not choose" their host countries and he called on other European Union states to do more.
Germany expects 800,000 migrants and refugees to arrive this year. Police said the number of arrivals more than doubled on Wednesday to 7266.
The head of the German Office for Migration and Refugees resigned for personal reasons after being criticised for slow processing of applications from a record number of asylum seekers.
Mr de Maiziere said Germany temporarily suspended the border with Austria "first", implying that more could follow.
For migrants, the announcement means Germany is not pursuing an open-door policy. After weeks of confusion, Berlin is now sending out the clear message that people have to apply for asylum in the first EU country they arrive in.
They will then be sent elsewhere in Europe according to a strict quota system.
Many migrants have been refusing to register in countries such as Greece or Hungary, fearing it will stop them being granted asylum in Germany or other EU states.
The possibility that Germany might suddenly decide to control its other borders was aimed to help jolt EU partners into action. But EU interior ministers this week failed to agree on a quota system designed to spread the burden.
A record 300,000 people have fled to Europe via Greece this year, according to the International Organisation of Migration.
More migrants coming
Undeterred by the problems faced by refugees and migrants at the gates of Europe, more have been arriving at the Greek port of Piraeus from Lesbos island, a short boat ride from Turkey.
Others are waiting outside Europe to attempt the hazardous journey that has cost thousands of refugees their lives.
"It would be very dangerous, but if you make it, the reward is great, the whole world will open up for you," Yousef Hariri, a refugee from Deraa in Syria, said at a refugee camp in Jordan.
In Istanbul, hundreds of Syrians and other migrants thronged a small park in the city centre hoping for a last chance to reach Europe before poor weather makes their favoured Aegean Sea route to Greek islands too dangerous to undertake.
Greece said large groups of refugees from Syria may be about to try to cross its far northeastern land border with Turkey, a relatively new entry point. Much of the frontier is fenced.
More than 116,000 more refugees and migrants have arrived in Italy.
Xenophobic views criticised
The Hungarian Prime Minister Viktor Orban, who has blamed Berlin for the wave of migrants after Merkel rolled out the welcome mat for Syrian refugees, said Muslims would end up outnumbering Christians in Europe if the policy continued.
"I am speaking about culture and the everyday principles of life, such as sexual habits, freedom of expression, equality between men and woman and all those kind of values which I call Christianity," Orban said in an interview.
The United Nations human rights chief, Zeid Ra'ad al Hussein, denounced "callous, xenophobic and anti-Muslim views that appear to lie at the heart of current Hungarian government policy".
"Europe was created to knock down walls, not to build them," Italian Prime Minister Matteo Renzi said.