A young Syrian boy sleeps on his father's shoulder after dozens of migrants unexpectedly disembarked a train from Budapest's Keleti station at the railway station of the airport in Frankfurt, Germany, early morning Sept 6, 2015. [Photo/Agencies]

They seemed dazed by the calls of "welcome to Munich," from the few dozen well-wishers remaining at around midnight, as well as by their determination to thrust chocolate bars, bananas or bread rolls into their hands.

A similar total is expected to arrive in Munich later on Sunday.

Munich police said Arabic-speaking interpreters were helping refugees with procedures at the emergency registration centres. The seemingly efficient Austrian and German reception contrasted with the disorder prevalent in Hungary.

"It was just such a horrible situation in Hungary," said Omar, arriving in Vienna with his family.

German Interior Ministry spokesman Harald Neymanns said Berlin's decision to open its borders to Syrians was an exceptional case for humanitarian reasons. He said Europe's so-called Dublin rules, which require people to apply for asylum in the first EU country they enter, had not been suspended.

"The Dublin rules are still valid and we expect other European Union member states to stick to them," he said.

After days of confrontation and chaos, Hungary deployed more than 100 buses overnight to take thousands of the migrants who had streamed there from southeast Europe to the Austrian frontier. Austria said it had agreed with Germany to allow the migrants access, waiving the asylum rules.