Chaotic scenes were reported across central Europe as thousands of migrants took to railways to complete their journey from Hungary to Germany. Budapest's main train station was temporarily evacuated and all rail traffic suspended as hundreds of asylum seekers tried to board carriages directed to Austria and then onwards to Bavaria.

Migrants reportedly chanted "Freedom! Freedom!" and "Germany! Germany!" as security forces moved to push them out of the Keleti station. The terminal reopened about an hour later with police deployed to keep the refugees out of the building.

The station had become a magnet for migrants as Hungarian authorities appeared to have loosened controls on train boarding, allowing on also people without EU visas. Several migrants outside the building told an AP reporter they bought tickets after being told by authorities they would have been granted free passage.

The move was criticised by Vienna, where more than 3,600 migrants arrived via train from Hungary on 31 August. "Allowing them to simply board in Budapest ... and watching as they are taken to the neighbour [Austria] — that's not politics," Austrian chancellor Werner Faymann told state broadcaster ORF.

Many of those who arrived at Vienna's Westbahnhof station, continued on towards Germany, with local police admitting they lacked the manpower to control the mass flux. Up to 2,000 arrived on 1 September at Munich train station, where they were met by authorities that provided water and medical aid. Police in the city thanked on Twitter the many volunteers who took to the station all sort of commodities, from food to baby diapers.

Bavaria social affairs minister Emilia Mueller said refugees were to be taken to a former barracks near Ingolstadt which have been turned into a reception centre. Others were taken to gym halls in the towns of Breclav and Hodonin, The Local reported.

The German interior ministry denied it had suspended EU regulations requiring asylum seekers to register in the first European country they arrive in, as it appeared the government had suggested earlier. The Dublin rules are still valid and we expect European member states to stick to them. Whoever comes to Hungary must get registered there and go through the asylum procedure there," a spokesman told Reuters.

Meanwhile, chancellor Angela Merkel repeated appeals for each EU state to take in a quota of refugees. "For those refugees who are being persecuted or have fled war, there should be a fair distribution in Europe based on the economic strength, productivity and the size of each country," she said at a joint press conference with Spanish prime minister Mariano Rajoy.

Hungarian prime minister Viktor Orban has announced talks with his European counterparts to discuss the crisis were to be held in Brussels later this week.

Tens of thousands asylum seekers fleeing war and poverty in the Middle East and Africa have travelled from Greece to Macedonia and then on to Serbia and Hungary, hoping to reach Germany and other northern EU states in recent months. Hundreds of thousands of have reached the borders of the 28-nation bloc this year, and more than 2,000 have died trying – most drowning while attempting to cross the Mediterranean on rickety boats.