Interior Minister Thomas de Maiziere said trains between Austria and Germany would be suspended for 12 hours "to return to orderly procedures" for entering the country.
Millions of Syrian refugees have been waiting out the war in neighboring states. As the fighting grinds on, and Europe starts to open the doors, additional waves of refugees may head north.
The president of the European Union is calling on countries to welcome their share of what the U.N. predicts will be at least 850,000 migrants over the next two years.
The migrant crisis has placed stress on infrastructure in Greece, Macedonia and Hungary. It has also highlighted divisions between European Union countries.
Groups of the refugees earlier had left a rail station and stopped train and begun walking toward Austria. Also: The father of a 3-year-old Syrian boy who drowned in the Aegean Sea buries his family.
More than 1,000 weary Syrian refugees were greeted with food and applause at the Austrian border after arriving by busloads from a long, chaotic journey through Hungary.