All trains between Austria and Bavaria, the principal conduit through which 450,000 refugees have arrived in Germany this year, ceased at 5pm Berlin time.

Germany’s national railway says it has resumed train services from Austria after authorities ordered a temporary halt on Sunday evening.

“Further steps will be determined according to the number of refugees heading to the Czech Republic”, Chovanec said.

Travellers have been told to expect disruption to rail, road and ferry services between Denmark, Austria and Germany.

The main goal for now is to ensure that interior passages in the station remain open including access to platforms and that trains are boarded in an orderly and safe manner they said. Many of them are escaping war and violence in Syria, Iraq, Afghanistan, and other troubled areas.

Under European Union rules, the first country of entry is required to deal with an asylum-seeker’s request for protection, but Germany had waived the rule for Syrian refugees.

By evening a train took away 700 asylum seekers with it leaving about 300 at the station’s emergency shelter.

Austria has made clear that its border controls are aimed at slowing migrants rather than turning them away altogether, but the moves have effectively suspended a system of borderless travel within Europe known as Schengen.

The proposals have faced opposition from Eastern European countries.

The majority of migrants entering Germany make the journey through Greece, Macedonia, Serbia, Hungary, and Austria.

The commission said the aim would be to return to the normal situation of no border checks between member states of the Schengen zone “as soon as feasible”.

Smaller refugee groups continued to come to Saalbrucke on Thursday and some 200 asylum seekers were still waiting for their registration, local media reported.

“Until now everyone was being shuttled to Munich“, federal police spokesman Rainer Scharf said. Train lines between Austria and Germany reopened today morning apart from one line to Munich, that has been used by tens of thousands of migrants, which was still closed because of people on the track, a rail company spokeswoman said.

Meanwhile, the flow of migrants into Hungary hit another record on September 12 after a total of 4,330 migrants walked across the border with Serbia.

“These border controls should be an important signal to the world”, Interior Minister Johanna Mikl-Leitner told the broadcaster ORF late on Tuesday.