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.
So far in 2015, more than 200,000 people have reached Greece and another 100,000 reached Italy, the U.N. says. Germany expects as many as 800,000 new arrivals this year.
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.
Abdullah Kurdi, whose 3-year-old son's lifeless body was photographed facedown on a Turkish beach, says: "I hope the world will learn something from it."
Police in Budapest lifted a two-day blockade of the Keleti station, allowing migrants to enter. But some inadvertently boarded trains bound for a refugee camp outside the capital.