Austria and Germany have acted quickly and humanely in an emergency situation to help around 12,000 refugees, but now the time has come to move back towards “normality” and reinstate proper border controls, the Austrian chancellor has announced.

“We have always said this is an emergency situation in which we must act quickly and humanely. We have helped more than 12,000 people in an acute situation,” Chancellor Werner Faymann said.

“Now we have to move step-by-step away from emergency measures toward normality, in conformity with the law and dignity,” he added, following "intensive talks" with German Chancellor Angela Merkel and Hungarian Prime Minister Viktor Orban.

The emergency measured negotiated by Berlin and Vienna on Friday have allowed over 12,000 desperate refugees, stuck in the Hungarian capital and elsewhere across the country, to be swiftly transferred to Germany.

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Budapest passed a series of laws on Friday effectively sealing Hungary’s southern border to migrants, with some 140,000 having crossed it so far this year. Those who have arrived are being held in “transit zones” until their asylum requests are approved.

New laws once enacted will make illegal border crossings punishable by up to three years in prison and will make it a criminal offense to damage Hungary’s new barb-wire fence along its 108-mile border with Serbia.

Hungary criticised Germany, which itself is due to welcome 800,000 asylum seekers by the end of the year, for accepting requests, in the process bypassing the Dublin Regulation.

“As long as Austria and Germany don’t say clearly that they won’t take in any more migrants, several million new immigrants will come to Europe,” Orban told Austrian broadcaster ORF.

Germany wants to help Hungary set up EU centers, so-called hot spots where the refugees will be offered worthy conditions while filing their applications for asylum, Peter Altmaier from the German Chancellery told ZDF national public service television.

It is part of the effort that Germany is now undertaking in permitting officers to process applications of asylum seekers even if they have traveled through other EU countries first.

Meanwhile Germany continues welcoming those who arrived via Austria. Around 100 refugees arrived in Berlin on Monday morning traveling by coach. Two buses dropped off the refugees in the western district of Spandau, where the authorities set up a refugee camp last Thursday. The camp has a maximum capacity of 710 people, with 71 tents able to hold 10 people each. Five more buses are expected to arrive during the night dropping off a further 250 newcomers.

By Sunday night some 11,000 migrants arrived in Munich, where several hundred local residents welcomed the migrants with applause. Some in the crowd handed out donations to the refugees, including sweets for children and bottles of water for the thirsty. Some 460 people took the train to Frankfurt that evening, while over 1,000 went to Dortmund.

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But in Dortmund, the refugees received a less-warm reception as far-right protesters met them on arrival. Police were forced to intervene and arrested four violent supporters of the far-right party “Die Rechte”.

Police used pepper spray as they clashed with extreme right German youths, who tried to force themselves onto the platform. Three police officers and one bystander suffered injuries in clashes. Additionally, an unknown person set a fire to the school building earmarked for use as a refugee home.