Hungarian police have used tear gas and water cannons on hundreds of migrants who broke through a razor wire fence on the border with Serbia.
Meanwhile, thousands of refugees prevented from moving through Hungary are now taking a longer route into Western Europe through Croatia.
Frustrated migrants blocked on the Serbian side of the border threw plastic water bottlers at rows of helmeted riot police and chanted demands that the border be re-opened.
Police responded with tear gas but there were no apparent injuries.
Some woman pushed to the front of the crowd and held small babies and children above their heads as they faced police in an obvious appeal for mercy, but no one made it through.
The incident took place at a small border crossing in Horgos, a short distance from the main border crossing into Hungary
Hungarian authorities also said that they have arrested a total of 519 migrants who tried to cross the border since tough new laws went into effect on Tuesday that make it a crime to cross from Serbia anywhere other than at legal checkpoints.
Authorities launched 46 criminal prosecutions and found an Iraqi man guilty, the first conviction based on the new laws.
Hungarian media reported the judge ordered the man expelled from Hungary and banned him from returning for one year. It was expected that he would be returned to Serbia.
Televised images from a courthouse in Szeged earlier showed four Iraqi men who were charged with their hands tied in front of them and their shoelaces removed ahead of trial.
In the past few months, Hungary has become a main entry point into the European Union for migrants, many of them war refugees from Syria and Iraq, with more than 200,000 entering the country so far this year.
Almost all entered from the southern border with Serbia and passed through Hungary quickly on their way to Germany or other wealthy Western European nations.
Syrian President Bashar Assad has blamed Europe for the crisis, saying it’s a direct result of the West’s support for extremists in Syria over the past four years.
In an interview with Russian media, Mr Assad accused Europe of supporting “terrorism” and providing “protection for terrorists, calling them moderates”.
“How can one be indignant about a drowned child and remain silent about the deaths of thousands of children, elderly people, women and men killed by terrorists in Syria?” Mr Assad said.
Hungary’s foreign minister denied that closed borders and tough new laws signal callousness toward refugees, repeating the government’s claim that most of those entering Hungary are actually economic migrants.
“Based on our history, we are always in solidarity with the refugees,” Peter Szijjarto said in an interview. “What we’re saying is that we cannot accept economic migrants because we cannot bear the burden of that.”
Most of the migrants who had hoped to cross into Hungary were still trapped along the border in Horgos, Serbia, however.
Many were confused about whether to keep waiting or to try to enter the EU through Croatia, a longer and less direct path into Western Europe.
Melita Sunjic, a spokeswoman for the UN refugee agency, said that early in the day the migrants were refusing to leave the border but changed their minds because of news and rumours going around that Croatia’s borders were open.
Most hope to reach Germany, where Chancellor Angela Merkel’s government has said it expects some 800,000 refugees to arrive in Germany this year alone. The vice chancellor has said the number could even reach one million.
At least two buses with about 100 people were seen leaving for the Croatian border from Kanjiza, a Serbian town on the border with Hungary.
About 300 crossed into Tovarnik, Croatia, after they were bused to the Serbian border town of Sid on an all-night ride from Macedonia.
Croatian Prime Minister Zoran Milanovic criticised Hungary’s decision to seal its border with Serbia for migrants and said Croatia will not do the same.
“We are ready to accept these people, regardless of their religion and the colour of their skin, and direct them to the destinations where they wish to go, Germany and Scandinavia,” Mr Milanovic told Parliament.
“Barbed wire in Europe in the 21st century is not an answer, it’s a threat,” Mr Milanovic said.
Migrants have avoided Croatia in the past because they must still go into Hungary or Slovenia before reaching Austria or Germany.
Elsewhere in Europe migrants remained on the move.
Greek police said about 5,000 refugees and migrants crossed the country’s northern border with Macedonia in the 24 hours from Tuesday morning to Wednesday morning.
Meanwhile, Austria began selective controls of vehicles at three main border crossings with Hungary as it tries to impose some order over the stream of people.