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Croatia has banned Serbian vehicles from entering its territory in response to a Serbian ban on Croatian cargo traffic in a bitter dispute over the flow of refugees across the border.
"Our border is ready and open for any other car without Serbian registration. Buses with Serbian registration will not enter into Croatia," Croatian Interior Minister Ranko Ostojic said.
Ostojic said there had been "a problem with passports" but confirmed that Serbian citizens were still free to travel across the border.
Serbia issued its ban on Croatian cargo traffic and goods late on Wednesday as relations plunged to their lowest since the overthrow of Slobodan Milosevic in 2000.
Meanwhile, Hungary has said it had received a record number of refugees in a single day, with most entering via Croatia.
Some 9,939 refugees arrived from Croatia on Wednesday, while 102 arrived from Serbia, AFP reported, citing Hungarian police.
German chancellor Angela Merkel has called on the US, Russia and the Middle East states to help Europe conquer the refugee crisis as she admitted "we are still far from where we need to be".
Ms Merkel said the way the crisis was tackled would shape Europe in the long term but said the extraordinary meeting of leaders in Brussels had sent out a signal of unity along with a pledge of more than €1 billion (£733 million) to fund new proposals to deal with the refugees.
She said all the participants of the EU meeting had recognised the scale of the refugee problem.
Europe has been warned it be must be braced for a surge of right-wing extremism across the continent unless the refugee crisis is dealt with properly.
European Commission Vice President Frans Timmermans said EU borders needed to be better controlled to deal with the hundreds of thousands fleeing war and poverty in the Middle East, Asia and Africa.
An extra €1 billion (£733 million) has been pledged by EU leaders to help tackle the refugee crisis.
European Council President Donald Tusk said the money will be used to help Syrian refugees in the Middle East and distributed via the UN High Commissioner for Refugees and the World Food Programme.
The figure was agreed following an emergency meeting of EU leaders in Brussels, where a number of other measures were agreed.
Mr Tusk said the current chaos on EU borders must end and that "hotspots" would be set up by the end of November.
"The measures we have agreed today will not end the crisis but they are all necessary steps in the right direction," he said.
European leaders are meeting in Brussels to try to repair the deep divisions that have opened up over how to deal with the refugee crisis.
Whilst EU ministers have agreed to relocate 120,000 refugees and migrants, in reality more than half a million have reached the continent with thousands more arriving daily.
Hungary, Poland, the Czech Republic and Slovakia oppose mandatory quotas, with the latter threatening legal action over the decision.
Britain has an opt out from the compulsory quotas but David Cameron has faced criticism for not doing enough to help the crisis. Today, he offered an additional £100m to help refugees in camps near Syria.
A lack of controls at the external borders means refugees and migrants are arriving into the EU far faster than politicians can agree what to do with them.
ITV News' James Mates reports from Brussels:
Angela Merkel has urged European leaders to prove "we can do this" as she arrived for an emergency EU summit on the refugee crisis.
The German Chancellor, who has faced criticism from some European nations for her more open stance to Syrian refugees, stressed that the continent needed to work together to deal with the issue.
Some eastern European leaders argued that Germany's decision to accept tens of thousands who were travelling through the continent had encouraged more to make the journey.
"Faced with a great challenge, it cannot be that Europe says: 'We can't handle this'," Mrs Merkel told reporters.
"That's why I say again and again: We can do this," she added.
Hungary's Prime Minister Viktor Oban has suggested other European nations should "defend" Greece's borders from refugees, as he arrived for a summit of EU leaders in Brussels.
Mr Oban, whose country opposed plans for the distribution of 120,000 refugees from Greece and Italy on Tuesday, told reporters: "I think if the Greeks are not able to depend their own borders, we should ask kindly - because Greece is a sovereign country - let other countries of the European Union defend the Greek border."
Mr Oban has been an outspoken critic of the EU's handling of the refugee crisis, and has said he will propose a global contingent to deal with it at the UN next week.
Latest ITV News reports
The latest EU emergency summit has to done very little to solve the refugee crisis other than create bitter arguments between members.
European leaders have been told their collective pledge of more than one billion euros will not end an accelerating refugee crisis.