Between midnight and 3:00 am alone, more than 1,700 people crossed the border at Nickelsdorf in eastern Austria, police said.
Early on Thursday morning, there were around 2,800 people at Nickelsdorf, receiving food, temporary shelter and waiting for special buses and trains to take them to Vienna and beyond. Most had slept out in the open during the night, in cold conditions.
The situation was however calm and people were exhausted but "very happy to be in Austria," said Christian Knopf, in charge of coordination.
As at the weekend when 15,000 people streamed into Austria and in recent days as thousands more have arrived, all but a handful continue their journey further north, mostly to Germany.
At the weekend, Austria decided to allow refugees to enter the country freely to help relieve a near-explosive situation in Hungary where 50,000 migrants arrived in August alone.
Chancellor Werner Faymann has said that border controls will return to normal but this has not yet happened. A government coordination meeting on Thursday was to discuss the next steps.
Austrian police said that those arriving had generally crossed into Hungary from Serbia less than 24 hours before, many taking trains to Budapest and then changing onto other trains to Hegyeshalom near the Austrian border.
Volunteers at the border said they are bracing for a renewed spike in numbers in the coming days as many migrants rush to enter Hungary before tough new laws there outlawing crossing the border come into force on September 15th.