It is understood all traffic has been banned on roads heading towards seven crossings into Serbia.
Some were trampling each other in a rush to get on the few available buses and trains, and dozens were injured in the mayhem.
The refugees turned to Croatia after Hungary erected a barbed wire-fence and took other tough measures to stop them from using it as a gateway into Western Europe.
The UN's special representative for international migration Peter Sutherland said countries needed to work together.
"Europe is a big place," he said, "and there are many places within it where a better life can be provided."
'Full capacity'
Hungarian officials hailed their success in putting a halt to the influx and moved ahead with plans to build more border fences.
But leaders in Croatia pleaded that their country was at full capacity and unable to cope with waves of people fleeing war and poverty in the Middle East and Africa.
Croatian interior minister Ranko Ostojic said he had a message for migrants - do not try to go to Western Europe through his country.
“Don’t come here any more. Stay in refugee centres in Serbia and Macedonia and Greece,” he told reporters. “This is not the road to Europe. Buses can’t take you there. It’s a lie.”
Hungary sealed off its border with Serbia this week with a razor-wire fence and began arresting people who tried to cross.
Police used tear gas, batons and water cannons on those who tried to push open a border gate on Wednesday.
9,200 refugees in 48 hours
Croatia represents a longer and more difficult route into Europe, but those fleeing violence in their homelands had little choice.
By late yesterday a total of 9,200 people had entered the country in just 48 hours, police said, and other groups were trying to cross into neighbouring Slovenia and Hungary.
Slovenia, like Hungary, appeared unwilling to take in the inflow, with Slovenian police saying those arriving from Croatia would simply be sent back there, according to the country’s state news agency.
Croatian president Kolinda Grabar Kitarovic called on the military to be on higher alert and to act if needed to protect the border from the refugees.
After bus trips through Serbia, many migrants crossed fields on foot to enter Croatia, where dozens of police at first directed them to trains and buses heading to refugee centres.
Authorities warned them to avoid walking in areas along the Serbian border, where there are still mines left over from Balkan wars.
Soon matters got out of control, and hundreds of angry asylum seekers pushed through police lines in the eastern Croatian town of Tovarnik after waiting for hours in the hot sun, demanding to be allowed to move on toward Western Europe.
More than 2,000 men, women and children had been stuck at the local railway station for hours. When buses finally arrived, groups charged toward them, overwhelming Croatian police.
The situation calmed down but some refugees moved off on foot, with police unable to stop them.
Families separated
In Croatia’s north, police in the town of Batina struggled to cope as hundreds of other asylum seekers came over a Danube River bridge after sent on buses by Serbian authorities.
Some families were separated as dozens of policemen tried to establish order.
As an EU member state, Croatia is required to register the asylum seekers. But almost all are trying to reach Germany or elsewhere in Western Europe, and want to move through quickly without a paper trail.
While many refugees quickly decided to switch routes and try their luck through Croatia, others found themselves stranded in Serbia.
“We’ve run out of money and we only know the way through Hungary,” said Mohamed Jabar, from the Iraqi town of Diyala, who was travelling with a son in a wheelchair and other family members.
“All the other ways are unknown to us. They say ... there is a way through Croatia but who will welcome me there?”
Hungary has faced strong international condemnation for its handling of the crisis. UN Secretary General Ban Ki-moon called its use of water cannons, tear gas and baton-wielding riot police unacceptable.
Hungarian foreign minister Peter Szijjarto rejected the criticism.
“I find it bizarre and shocking that certain esteemed international figures have stood on the side of people who for hours were throwing stones and pieces of cement at the Hungarian police,” he said.