Migrants stranded in Croatia have been making renewed efforts to head north despite moves by Slovenia and Hungary to hold them back.
Slovenian police used pepper spray on Friday night to disperse a group trying to cross from Croatia.
Hungary, meanwhile, accused Croatia of breaking international law after asylum seekers were sent over the border without first being registered.
The EU, which is divided on the crisis, is to hold emergency talks next week.
Overnight, thousands of migrants trying to pass through the Balkans to reach northern EU states spent the night at railway stations or sleeping alongside roads.
In a day of chaos and confusion on Friday, people were shunted from one border to another as governments remained split over how to handle the crisis.
Thousands entered Croatia from Serbia earlier this week after Hungary fenced off its Serbian border and sealed shut the previous route north.
Croatia had initially said migrants would be welcome, but on Friday said it was overwhelmed after seeing 17,000 arrivals since Wednesday. It has closed all border crossings with Serbia except the main road linking Belgrade and Zagreb.
Croatia then began sending people north without registering them, angering Slovenia and Hungary. All three are EU states but asylum seekers particularly want to reach Hungary and Slovenia, which are in the borderless Schengen Area.
Hungarian authorities said a train carrying more than 1,000 migrants and about 40 Croatian police had arrived unannounced. Officials said the officers were being sent back to Croatia and the migrants were being sent by bus to registration centres near the border with Austria.
Austria, however, said it had not co-ordinated with Hungary to take the migrants.
It said it reserved the right to deny entry to any migrants who did not request asylum because they wanted to continue travelling north to Germany or elsewhere.
There was tension in the village of Harmica on the Slovenian border with Croatia where people were stranded when all rail services were suspended.
After a stand-off, Slovenian riot police used pepper spray against a crowd trying to cross the border on foot.
Bostjan Sefic, state secretary at the Slovenian interior ministry, accused Croatia of breaking the rules of both the EU and the Schengen agreement by deciding to stop registering migrants.
However, Slovenian Prime Minister Miro Cerar later said that if the pressure of arrivals became too great, it might seek to form corridors allowing migrants safe passage.
EU regulations dictate that refugees must register and claim asylum in the first member state they reach.
But many migrants and refugees wish to continue on to countries in northern Europe such as Germany and Sweden.
Europe is experiencing a huge influx of asylum seekers - many fleeing conflicts in Syria, Iraq and Afghanistan - but the EU has been strongly criticised for its failure to co-ordinate a response.
Interior ministers will hold an emergency meeting on Tuesday in another attempt to agree on relocating migrants with binding quotas for each state.
The next day, EU leaders will hold an extraordinary summit on migration.
In his invitation to leaders, European Council President Donald Tusk called the crisis a test of the EU's "humanity and responsibility".
He said migration would be a challenge for "many years to come".
Migrant crisis in Europe: Key dates
--13 July: Hungary starts building razor-wire fence on border with Serbia
--25 Aug: Germany says all Syrian refugees can apply for asylum there, regardless of which EU country they first entered
--2 Sept: Image of body of three-year-old Syrian Alan Kurdi, washed ashore in Turkey, moves public opinion worldwide
--12 Sept: Record 4,330 migrants cross into Hungary
--13 Sept: In a switch of policy, Germany introduces border controls with Austria - other EU nations later impose their own controls
--15 Sept: Hungary enforces tough laws on migrants crossing its border fence, prompting thousands to turn to Croatian route
--18 Sept: Croatia transports migrants over its border into Hungary, where Hungary rushes to build new fence