About 6,500 refugees have arrived at Austrian border from Hungary early on Saturday morning, Austrian police say the number is likely to rise during the day.
"Our biggest problem is that the Hungarians - after checking back with Budapest, are refusing to let our buses enter their territory and pick up the refugees," said Hans Peter Doskozil, chief of the police in the Austrian province of Burgenland.
"We offered them that they can bring the refugees directly to the trains, or to the shelter, but they just stop the buses on the Hungarian side, everyone has to get off in the rain," he said adding that two special trains taking refugees from Austrian border to Vienna were about to arrive.
The highway was closed for all traffic into Austria to move the refugees on. Some Australians were waiting for holding signs that read “Refugees welcome.”
"We're happy. We'll go to Germany," said a Syrian man who gave his name as Mohammed.
After days of confrontation, the Hungarian government announced on Friday it would deploy buses to transport thousands of refugees to the Austrian border. Including hundreds who opposed attempts to register them in Budapest, and had begun walking to the border.
The Austrian Chancellor, Werner Faymann, said that they decided to let the refugees enter, and that thousands of refugees had reached Austria early on Saturday morning by buses.
“Because of today’s emergency situation on the Hungarian border, Austria and Germany agree in this case to a continuation of the refugees’ journey into their countries,” wrote Faymann in a Facebook post.
Social media and news channels showed the footage of people who were met by Austrian authorities.
Austrian Foreign Minister Sebastian Kurz said on Saturday, the situation of thousands of refugees stranded at a station in Hungary was a “wake up call” for Europe.
"This has to be an eye opener how messed up the situation in Europe is now," Kurz said as he talked with his EU peers about refugee crisis.
"I hope that this serves as a wake up call that cannot continue."
On Friday, approximately 1,200 refugees started a 170-km journey to the Austrian border. While they were boarding the buses, many of the refugees smiled and said goodbye to the Hungarian volunteers, who had given them food and water.
Many people had been camped in front of the central railway station before trains heading to Austria and Germany were cancelled by authorities, after today's news Keleti station quickly emptied out as refugees left for the Austrian border.
More than 140,000 refugees have entered Hungary so far this year, through the Europen Union’s external border with Serbia. There may be also refugees who entered without registering. The Hungarian government is building a 3,5-metre (11,5-foot) high wall on the border.
Lawmakers adopted some measures on Friday, creating “transit zones” to hold asylum seekers while their applications are being processed. The refugees who cross the border without permission or damage the fence will face jail terms.