Hungary has closed the main border crossing for migrants entering from Serbia as Europe's passport-free zone creaked under the reinstatement of border controls by Austria, Slovakia and Germany.
The growing tensions at the heart of the EU's flagship Schengen area ramped up the pressure on interior ministers holding emergency talks in Brussels on the unprecedented flood of people fleeing Syria and other war zones.
A day before Hungary has vowed to begin arresting illegal migrants, police fenced off a gap in the razor-wire barrier with non-EU Serbia that hardline Prime Minister Viktor Orban's government is racing to complete, leaving dozens of migrants stranded.
Most of the refugees are trying to get to economic powerhouse Germany, which on Sunday abandoned its open-arms policy and reintroduced border checks amid claims it would take in one million refugees this year.
Despite the escalating crisis and a shift in public opinion after heart-wrenching pictures of a drowned Syrian migrant child - one of more than 2700 people to have died crossing the Mediterranean this year - EU ministers remained divided on a solution.
"If we do not take decisions then chaos is the consequence ... there will be a domino effect and we can forget Schengen," said Luxembourg minister Jean Asselborn, who chaired the EU talks in Brussels.
The United Nations refugee agency warned the confusion surrounding border policies in Europe could leave migrants, many of whom have made gruelling treks through the continent, in "legal limbo".
At Hungary's Roszke border crossing, several dozen migrants including many children, some in pushchairs, were stuck on the Serbian side of the border, with several women crying, after police shut the border, AFP journalists saw.
Hungary is on the frontline of Europe's migrant crisis, with almost 200,000 people travelling up from Greece through the western Balkans and entering the country this year, most of them seeking to go to northern Europe.
But Hungary's neighbours are now feeling the strain, with Germany shocking the EU on Sunday when it admitted that Europe's biggest migration crisis since World War II meant it had to reinstate border controls eliminated under Schengen in the late 1990s.
Austria and Slovakia pounced on the U-turn by Chancellor Angela Merkel's government - which had previously said it would throw open its doors to Syrian refugees - to reinstate their own border checks.
"We will proceed as Germany did," Austrian Interior Minister Johanna Mikl-Leitner said in Brussels.
Poland said it was considering similar steps while the Netherlands said it would have "more patrols" on its frontiers.
EU states can impose temporary controls for security reasons under the Schengen treaty but there are fears the very ideal of a borderless Europe could collapse.
Divisions are also rife among the ministers on a plan unveiled last week by the European Commission to redistribute 160,000 refugees across the continent to relieve pressure on "frontline" countries such as Italy, Greece and Hungary.
Several Eastern European states such as Hungary, the Czech Republic and Slovakia oppose compulsory quotas for relocating the refugees.
On Monday the EU ministers formally approved an initial plan to relocate 40,000 of the refugees - a proposal which was first raised in May and then put on hold by EU leaders - but struggled to get unanimous approval for the plan for the other 120,000.
However the EU did approve plans for military action against people smugglers in the Mediterranean, seizing and if necessary destroying boats.
Honking cars with stressed drivers have been banked up for kilometres at an Austrian-German road crossing after Berlin reimposed border checks in the face of a massive refugee influx.
Two German police officers on Monday checked the identity papers of the steady stream of drivers and passengers on a bridge where the traffic bottle-necked into a single lane.
"It's like being back in the 1980s," complained one of the drivers caught up in the snarl, 71-year-old German pensioner Helmut Zimmermann.
"I would never have imagined such poor organisation."
Two decades after western Europe began to abolish internal border controls, Germany installed impromptu checkpoints again, grappling with the continent's biggest wave of asylum-seekers since World War II.
Chancellor Angela Merkel's spokesman on Monday said that Germany was not slamming its doors to refugees but argued the measure was needed to restore order to the asylum process.
The two police officers were checking papers and radioing their colleagues further down the road telling them which motorists to pull aside for closer questioning.
No refugees could be seen, either in vehicles or on foot, at the Freilassing border point.
Zimmermann said he had crossed the border from his small German hometown of Piding in the morning, only to be caught up in the wait on the way back.
"I always drive across to Austria to buy cigarettes and fill up on petrol," because of the lower prices, he told AFP.
He welcomed the new controls, but not the way they were being carried out, grumbling that "it couldn't possibly work smoothly with just two police officers on that bridge".
The police at the crossing, meanwhile, said the effort hadn't yet netted any people traffickers, after several were arrested the previous day.
"We haven't seen any smugglers for hours," said one of the officers, declining to give his name.
"They would be pretty stupid to still be arriving now. They would get a free one-way trip to prison".