Budapest, Hungary (BBN)-Waves of migrants seeking to enter the EU from the south-east have been shunted from one border to another as governments disagree over the crisis.
Croatia reversed its open-door policy after 17,000 arrivals since Wednesday, reports BBC.
It is now sending thousands of migrants north, angering Slovenia and Hungary.
Hungary, which is putting a fence on its border with Croatia, is reportedly sending new arrivals on to Austria.
Two EU crisis meetings will take place next week.
Many of the migrants are fleeing conflicts in Syria, Iraq and Afghanistan.
Thousands began entering Croatia from Serbia this week after Hungary closed its Serbian border, and cut off the previous route north.
Croatia had initially said the migrants would be welcome, but on Friday it said it was overwhelmed and would not become a "migrant hotspot".
Interior Minister Ranko Ostojic said that more than 17,000 migrants had arrived since Wednesday morning and that 3,000 had now crossed into Hungary.
Hungary reversed its stance from earlier in the week and let the new arrivals in.
One train carrying up to 1,000 migrants to Hungary was seized by authorities there and the driver arrested, the head of Hungary's disaster unit said, according to Reuters.
Some 40 Croatian police were disarmed, the report said. Croatia later denied this and said the officers had returned to Croatia.
Hungary is now taking the migrants to two registration centres, close to the border with Austria.
Austria said it had no co-ordination with Hungary to take the migrants.
It reserved the right to deny entry to migrants who did not request asylum because they wanted to continue travelling north to Germany or elsewhere.
Separately, hundreds of migrants set off for Slovenia, to the west.
The BBC's Christian Fraser, at the Slovenia-Croatia border, said the number of migrants arriving was building on Friday evening.
Slovenian police pepper sprayed about 500 migrants at one bridge on the border, Associated Press reported.
IN OTHER DEVELOPMENTS:
Turkish police sealed off the road to Greece at the border town of Edirne after several hundred migrants tried to make the crossing
Germany is to set up a tent settlement to accommodate 5,000 people in Bavaria, the entry point for migrants coming from Austria
The International Organisation for Migration said 473,000 migrants have crossed the Mediterranean to Europe this year, including more than 180,000 Syrians
German Foreign Minister Frank-Walter Steinmeier said EU members reluctant to accept migrant quotas might have to be over-ruled with a majority vote at a summit on 23 September
The latest EU figures show that in the second quarter of 2015, 213,200 first-time asylum seekers applied for protection, up 15 per cent on the first quarter and up 85 per cent on the same quarter in 2014
SLOVENIAN ANGER
Earlier, Hungary announced it was building a new fence along part of its border with Croatia.
It was Hungary's completion of a razor-wire fence along its border with Serbia earlier this week that forced Serbia to move migrants towards Croatia.
Hungary's new laws made attempts to cross its frontier illegal, and Foreign Minister Peter Szijjarto on Friday accused Croatia of encouraging "masses of people to commit a criminal offence".
Croatian officials said earlier that every border crossing with Serbia except the main road linking Belgrade and Zagreb - at Bajakovo - had been closed.
Many migrants who managed to enter were rounded up by Croatian police and sent to reception centres.
Some were taken to the capital, Zagreb, but many were also trying to get to Slovenia on foot.
The Slovenian interior ministry said it expected some 1,000 migrants to arrive in the next 24 hours.
Bostjan Sefic, state secretary at the Slovenian interior ministry, accused Croatia of breaking the rules of both the EU and the Schengen free movement agreement by deciding to no longer register migrants.
It has closed its rail service to Croatia.
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.
The crisis has challenged the Schengen regime, with Germany, Austria and Slovakia all reimposing checks on parts of their borders.
EU regulations dictate refugees must register and claim asylum in the first member state they reach.
But many migrants and refugees wish to continue on to Germany and Austria.
MIGRANT CRISIS IN EUROPE: KEY DATES
13 July: Hungary starts building razor-wire fence on border with Serbia
19 Aug: Germany says it expects to receive 800,000 asylum applications by the end of 2015
27 Aug: Bodies of 71 Syrian migrants found in lorry in Austria
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: Germany reintroduces border controls with Austria in shock migrant policy U-turn. Other EU nations also later resume controls
15 Sept: Hungary enacts tough laws on migrants crossing its new Serbian border fence. Thousands of migrants turn to Croatian route
18 Sept: Croatia transports migrants over its border into Hungary. Hungary rushes to build new border fence there
BBN/SK/AD