Hungary has suspended all traffic from its main rail terminal and cleared the station of hundreds of migrants trying to board trains for Austria and Germany.
Migrants chanting "freedom, freedom" congregated outside the station after being pushed out from the station building, joining hundreds more in what has become a transit zone and place of refuge for those fleeing Syria's war and other Middle East hotspots.
Police acted shortly after authorities announced over station loudspeakers that all trains would be stopped from leaving the station for an indefinite period of time.
Hundreds of passengers with travel documents and tickets remained in the cavernous station, some staring at information boards still showing arrival and departure times
Scuffles broke out earlier in the morning among some of the hundreds of migrants as they pushed towards metal gates at the platform where a train was scheduled to leave for Vienna and Munich, and were blocked by police.
Several said they spent hundreds of euro for tickets after police told them they would be allowed free passage.
The closure of the station appeared prompted in part by pressure from other EU countries trying to cope with the influx from Hungary.
Europe has been overwhelmed by a surge of migrants, with more than 332,000 arriving so far this year, according to the International Organisation for Migration.
Police in Vienna said that 3,650 migrants arrived from Hungary at the city's Westbahnhof station on Monday, with most continuing on towards Germany.
"Allowing them to simply board in Budapest... and watching as they are taken to the neighbour (Austria) - that's not politics," said Austrian chancellor Werner Faymann.
While critical of Hungary, Austrian authorities also acknowledged they were overwhelmed by the thousands who arrived by rail on Monday evening.
Police said they did not have the manpower to carry out effective controls, which normally would include turning back to Hungary those without proper travel documents who do not ask for asylum in Austria.
But in their search for human traffickers, they reimposed controls begun on Monday at some of the main road border crossings into Austria from Hungary.
Hungary's Utinform agency, which provides motorists with traffic news, said that vehicles entering Austria at the Hegyeshalom crossing were backed up for about three-and-a-half miles.
Chancellor Angela Merkel said Germany is not to blame for the stream of Syrian refugees in Hungary trying to board trains headed for Germany.
Hungary's government has pinpointed Germany's "more flexible attitude" towards Syrians as a problem that encourages migration. German authorities have advised officials not to send Syrians back to the first European Union country where they arrived, as EU rules stipulate.
Ms Merkel said that Syrians do have a high chance of getting asylum but "that should be no surprise ... and should actually be similar in every European country".
She said "the current rules are clearly not being practised". She said the answer is a common European asylum policy with a "fair distribution" of refugees across the 28-nation EU.
Many of the migrants have entered Europe through Greece and then travelled north through Macedonia and Serbia before reaching Hungary.
In Geneva, the UN's children's agency said the number of women and children fleeing through Macedonia has tripled in the past three months - up to 3,000 people a day are passing through and roughly one in eight is a pregnant woman.
Greece's coastguard, meanwhile, said it had rescued more than 1,000 migrants from the sea off its eastern Aegean islands in the last 24 hours.
And tensions are flaring once again at Greece's northern border with Macedonia, where about 1,500 migrants are waiting to cross the border and head north towards the more prosperous EU countries.
Fights and scuffles broke out among the crowd near the Greek village of Idomeni when hundreds of people, mainly from Afghanistan and Pakistan, attempted to rush the border being guarded by Macedonian police.
Macedonian authorities have been allowing small groups to cross at a time and head to the Gevgelija train station. Last month, Macedonian authorities briefly halted all crossings and used stun grenades and batons to push back the crowd.
Hungary later revealed more than 156,000 migrants have entered the country this year.
The interior ministry said around 142,000 people have requested asylum, including 45,000 migrants from Syria.
Hungarian prime minister Viktor Orban will meet with top EU officials on Thursday in Brussels about the crisis, including EU Commission president Jean-Claude Juncker, EU Council president Donald Tusk, and European Parliament president Martin Schulz.
Meanwhile, Hungary's defence minister said up to 3,500 soldiers could be sent to the southern border with Serbia to help with the migrants crisis.
Csaba Hende reassured politicians that troops would not use deadly force to disperse unarmed crowds of migrants.
Using troops at the border is one of several measures regarding migrants to be debated this week by the Hungarian parliament. Others include longer prison terms for human traffickers and making it a crime to cut through the border fence or to enter Hungary anywhere except at official border stations.