Thousands of refugees arrived in Germany and Austria as part of coordinated efforts to deal with the growing influx, following days of high drama in Hungary. Thousands have crossed the border in the last few days as the EU migrant crisis intensifies.

Special trains carrying the exhausted refugees arrived in the German city of Munich and as many as 3,000 people are expected to reach Germany by the end of today, 6 September. Initially, the refugees were taken to a registration centre in Munich from where they will be sent to various shelters in other cities.

"The Dublin rules are still valid and we expect other European Union member states to stick to them," said German interior ministry spokesperson, Harald Neymanns insisting that the refugees need to apply for asylum in the first country of their arrival.

It is estimated about 6,000 asylum-seekers had passed through the Munich central station by the evening of Saturday, 5 September, authorities say. Along with providing food and water, they have been accommodated in makeshift arrangements. Arabic-speaking interpreters are also helping the refugees in order to deal with the situation.

"We are giving a warm welcome to these people today. We realise it's going to be a big challenge but everybody, the authorities and ordinary citizens, are pulling together," said Simone Hilgers, spokesperson for the agencies in Upper Bavaria which are helping the migrants.

In Austria, severe rain battered the migrants, carrying their meagre belongings in backpacks, in the early hours as authorities continued to struggle to provide resources for them. Austria's Red Cross is also providing medicines and other essentials.

"We have treated a two-day-old gunshot wound. We've seen eye injuries caused by stun grenades. We've seen children with severe bruises," said Red Cross spokesperson Andreas Zenker.

The refugees were taken by pleasant surprise as they were given a rousing welcome by Europeans in some cities holding signs of "Refugees Welcome".