At least 10,000 refugees have arrived in Austria on September 19, amid bitter rows among EU nations on how to handle the growing crisis.
The refugees had been sent from Croatia into Hungary, which in turn shipped them on to Austria.
Hungary accused Croatia of breaking the rules by failing to register the refugees.
Meanwhile, 26 refugees are missing after their boat sank off Greece.
Coastguards managed to rescue 20 people but were told the boat had been carrying 46 people when it sank off the Greek island of Lesbos.
Separately, a search is continuing for 13 people still missing after their boat sank in the same waters on September 19, killing a five-year-old girl.
On the same day, Austrian police said they were expecting at least 10,000 arrivals, while the head of the Austrian Red Cross, Gerry Foitik, later told Austria Presse Agentur (APA) that between 12,000 to 13,000 people had entered the country over the course of the day.
The deputy police chief of Austria’s Burgenland state, Christian Stella, told APA that Hungary had not given enough warning.
Austrian Interior Minister Johanna Mikl-Leitner accused neighboring countries of failing to follow EU rules, expressing concern that migrants were also arriving from Croatia via Slovenia.
One refugee, who crossed into the Austrian town of Heiligenkreuz from Hungary, told the Associated Press: “I feel like I’ve been born anew. It makes no difference whether I am delayed, whether I stay here two days. The important thing is that I’ve finally arrived and that I am now finally safe.”
Croatia has seen 20,000 refugees entering from Serbia since September 16 and, after initially welcoming them, said it was unable to cope and moved them on.
PM Zoran Milanovic admitted there was no agreement with Hungary.
“We forced them, by sending people up there. And we’ll keep doing it,” he said.
Hungarian Foreign Minister Peter Szijjarto branded Zoran Milanovic “pathetic”, adding: “Instead of honestly making provision for the immigrants, it sent them straight to Hungary. What kind of European solidarity is this?”
The Hungarian government accused Croatia of breaching international law by failing to register refugees and said all asylum seekers would be registered in Hungary before they could leave for northern Europe.
However, a number of refugees who reached Austria via Hungary ssaid they had not been registered in Hungary either, simply driven in buses across the country and told to walk over a railway line into Austria.
While Hungary continues to transport refugees arriving from Croatia, it is building a razor-wire fence on the border that will be completed soon.
Hungary says it will then enforce the same tough laws it introduced earlier this week on its Serbian border – where there is a similar fence – making crossing it a criminal offence.
However, government spokesman Zoltan Kovacs said that “at the moment” stopping the flow “seems to be impractical”.
Hungary’s government has declared a state of emergency at the Serbian border as tough new laws to stop refugees entering illegally took effect at midnight.
Hungarian police said they had arrested 60 people accused of trying to breach a razor-wire fence on the border with Serbia.
The state of emergency gives police extra powers and would allow troop deployments if parliament approves.
The EU states are facing a huge influx of refugees, many fleeing conflict and poverty in countries including Syria.
Meanwhile, Germany and Austria are calling for a special meeting of EU leaders next week to discuss the crisis.
German Chancellor Angela Merkel told a news conference that “this problem can only be solved together. It is a responsibility for the entire European Union”.
The EU’s border agency said more than 500,000 refugees had arrived at the EU’s borders in 2015, compared with 280,000 in 2014. The vast majority have come by boat across the Mediterranean.
A boat following the most popular recent route, between Turkey and Greece, sank on September 15 leaving 22 people dead, Turkish media reported.
Starting on September 15, the European Union has agreed to relocate 40,000 migrants from Greece and Italy to other EU states. However, it has yet to agree on mandatory quotas for a further 120,000 asylum seekers.
After the new Hungarian laws came into effect at midnight, police sealed a railway crossing point that had been used by tens of thousands of migrants.
Around midday there were tense scenes as hundreds streamed towards the fence, some searching for a way through and others starting a sit-down strike, throwing down food and water in protest at not being granted passage.
Hungarian authorities said more than 9,000 – a new record – crossed into the country before the border was closed on September 14. Some 20,000 crossed into Austria.
From September 15, anyone who crosses the border illegally will face criminal charges, and 30 judges have been put on standby to try offenders.
The laws also make it a criminal offence – punishable by prison or deportation – to damage the newly-built 13ft fence along Hungary’s 110 mile border with Serbia.
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