Scuffles have broken out west of the Hungarian capital, Budapest, after police tried to force migrants off a train at a refugee camp.
Amid chaotic scenes, police ordered journalists from the scene at Bicske, declaring it an "operation zone".
The train had left Budapest hours after police let migrants into the railway station following a two-day stand-off.
Meanwhile, there have been sharp disagreements among European leaders over how to deal with the crisis.
In Brussels, Hungary's Prime Minister Viktor Orban described the situation as a "German problem" as Germany was where those arriving in the EU "would like to go".
But European Council President Donald Tusk said that at least 100,000 refugees should be distributed across EU states.
The human cost of the crisis was put into sharp focus on Wednesday when five children were among 12 migrants who drowned in Turkish waters while trying to reach Greece.
Images of the washed-up body of three-year-old Alan Kurdi, who died alongside his mother and five-year-old brother, circulated widely on social media.
Earlier on Thursday, migrants who had been camped outside Budapest's Keleti railway station surged on to the platforms as soon as police withdrew.
International services were suspended at Budapest's station but hundreds crammed on to the first train hoping it would take them to the Austrian border.
Instead, the train stopped at the Hungarian town of Bicske about 40km (25 miles) west of Budapest which hosts a major refugee camp, and police lined the platforms.
Some migrants at first left the train but then forced their way back on when they realised where the authorities wanted them to go.
They fear that registering at the camp will make it harder for them to seek asylum in Germany and other countries.
Back in Budapest, about 2,000 migrants are still camped outside the Keleti station with more in nearby John Paul II square and at Nyugati railway station across the city.
"I think (the train) was a trick by the government, the police and the train company, " said Marton Bisztrai, a volunteer at Keleti.
"The train looked like it was going to Germany."
The number of migrants entering Europe has reached record levels this year. Germany expects to take in 800,000 asylum seekers this year - four times last year's total.
The surge in numbers has created tension and disagreement over EU migration policy. Germany has been prepared to accept large numbers of asylum seekers, but other countries have not.
During a tense press conference in Brussels with European Parliament President Martin Schulz, Mr Orban, who heads the anti-immigration Fidesz party, said Hungarians "were full of fear because they see that the European leaders... are not able to control the situation".
"Nobody would like to stay in Hungary, neither in Slovakia nor Poland nor Estonia. All of them would like to go to Germany. Our job is only to register them," he said.
Mr Tusk took Mr Orban to task for saying in a newspaper interview that Hungary was being "overrun" with refugees who threatened to undermine Europe's Christian roots.
"Referring to Christianity in a public debate on migration must mean in the first place the readiness to show solidarity and sacrifice," he said.
Mr Tusk's call for at least 100,000 asylum seekers to be redistributed across EU states is a sharp increase on a previous European Commission target of 40,000.
