Migrants from Middle Eastern countries camp outside a railway station, near the border crossing between Serbia and Croatia, on Thursday.

Reuters/Sid, Croatia

More than 5,000 migrants have entered Croatia since Hungary sealed its southern border with Serbia, police said on Thursday, seeking new routes through the Balkans to western Europe.

With their path north from Serbia into Hungary - and the European Union - blocked since Tuesday, migrants have simply turned west to the Croatian frontier.

The influx, which Croatia says it will not halt, puts tiny Slovenia next in line to receive the thousands of migrants, many of them refugees from the Middle East, trying to reach Austria then Germany and other more prosperous countries of northern and western Europe.

"We are tired. We are exhausted. We have been travelling for 10 days. We just want to pass to through Croatia and go to Germany," said 19-year-old Salim from Syria who crossed at the Serbian border town of Sid.

Hungary's crackdown has been decried by the UN and human right groups.

Hundreds of migrants, mainly young men, clashed with Hungarian riot police on Wednesday over a fence that Hungary has built the length of the frontier, the latest violence in a migration crisis that has seen hundreds of thousands of people from the Middle East, Africa and Asia reach Europe's shores.

"The migrants can be seen entering Croatia around several crossing points," police said, putting the figure since early Wednesday at 5,650.

Croatia, the EU's newest member, says it will not halt their passage. But Slovenia, which unlike Croatia a member of Europe's Schengen zone of border-free travel, has ruled out creating a "corridor" for migrants. It says any asylum seekers will be accommodated in Slovenia and others turned back.

Croatia said it was considering new measures to cope with the inflow.

Croatia: Austria is bigger

"Croatian police have full control on the border, but if the migrants continue flowing in from Serbia in large numbers, we will have to consider other ways of handling the situation," Interior Minister Ranko Ostojic said during a visit to eastern Croatia late on Wednesday.

He did not specify how this would be done, but said the EU would have to handle "hot spots" before the migrants reach Croatia.

Croatia said it could cope with several thousand people, but not with tens of thousands. The migrants are at the moment being transported to reception centres near the capital Zagreb.

Croatian Prime Minister Zoran Milanovic met Austrian Chancellor Werner Faymann, who was also due to meet his Slovenian counterpart Miro Cerar in Ljubljana.

"We agreed on certain things," Milanovic told a government session. "Austria is a bigger country, but they also have their limitations to cope," he said. "If the number of migrants continues increasing, I'm not sure we will be able to register them all."

Many appeared to be arriving from the Serbian-Hungarian border, where their path is blocked by Hungarian riot police, a metal fence and strict new laws that have seen asylum claims rejected in quick succession and those caught illegally crossing the border expelled.

An official with the UN refugee agency, UNHCR, said there were "significantly less people" waiting at the Serbian border in the vain hope of entering Hungary.