Hungary has declared a state of emergency, leaving thousands stranded on its border with Serbia.
The first refugees have crossed the Serbia-Croatian frontier, carving out a new route through Europe after Hungary sealed its borders.
The development came as German Chancellor Angela Merkel on Tuesday called for a special EU refugee summit, urging unity in the European response to the crisis.
Croatian police on Wednesday said they were registering refugees entering from Serbia and would transport them to reception centres near the capital Zagreb.
A police spokesman in the eastern border county of Vukovarsko-Srijemska confirmed an unspecified number of refugees had crossed into Croatia, after a Reuters news agency cameraman saw at least 100 walking through fields across the border.
Earlier on Wednesday, a group of 30-40 mostly Syrian or Afghan nationals arrived at the Serbian town of Sid near the Croatian border. They had travelled by bus from the Macedonian border at Presevo, 500km to the south.
Among the mixed group of men, women and children of all ages was Amadou, 35, from Mauritania in western Africa.
“We heard that Hungary was closed so the police told us we should come this way,” he said. “We don’t know what we should do now. Do we have to catch a boat?”
He was pleased to hear there was no water to cross and it was only about 10km to the border. He was also surprised to hear the group was thought to be the first to attempt this route into northern Europe.
The new route takes the refugees to Croatia, from where they will have to travel through Slovenia to get to northern Europe.
Until this week, the vast majority of refugees travelled up from Greece, through Macedonia and Serbia into Hungary.
But Hungary sealed its southern border Monday as part of a wider crackdown on refugees entering the country.
Earlier on Tuesday, Hungary declared a state of emergency, and shut its border with Serbia leaving many desperate refugees stranded at the border.
Almost 10,000 people have also been detained for illegally crossing the border from Serbia, police said.
Hungarian Prime Minister Viktor Orban has indicated that asylum requests from refugees trying to enter Hungary from Serbia will be rejected, because Serbia is a safe country where refugees do not risk war or persecution.
Like others at the bus station in Sid, Amadou had never heard of Croatia and did not know it was in the European Union.
“We want to go anywhere there is peace,” he said. “There is so much suffering in Mauritania, so many problems for our family, no work.”
Slovakia has also started spot-checks at its borders with Hungary and Austria , fearing it could be a new transit point for refugees.
Austria posed new restrictions at its borders on Tuesday, as it struggled to cope with a backlog of thousands trying to reach Germany.
The AP news agency also reported that the temporary control imposed by Austria from midnight local time (2200 GMT) on the Hungarian border may also be extended to other nations.
Thousands of refugees have poured into Austria in recent days, rushing through Hungary ahead of a deadline that saw that country close its border with Serbia.
Merkel on Tuesday called for a special EU refugee summit, urging unity after an angry reaction to a suggestion by one of her ministers that countries that did not take in their share of asylum seekers could face financial penalties.
The proposal by Interior Minister Thomas de Maiziere was forcefully rejected by the Czech Republic and Slovakia, which are among Eastern European states that have resisted EU plans to share out refugees.
Merkel later took a more conciliatory tone, calling for Europe to come together on the refugee issue.
“I think we need to establish a European spirit again… I don’t think threats are the right way to achieve agreement,” she told a news conference with Austrian Chancellor Werner Faymann, whose country is also in the front-line of the refugee crisis.
Facing opposition from ex-communist states, EU ministers failed on Monday to break a deadlock over sharing responsibility for accepting some of the hundreds of thousands who have sought asylum in Europe.
They have been summoned back to Brussels next Tuesday but diplomats said those calling for national refugee quotas were loath to simply outvote their eastern neighbours.
De Maiziere said an agreement was still some way off.