Chancellor Werner Faymann said Austria would remove the emergency measures for asylum seekers “step by step”.
The easing of rules has meant thousands have been able to leave Hungary for Austria and Germany over the weekend.
Germany, where most of the migrants are headed, warned that its willingness to help “should not be overstretched”.
The German interior ministry said the decision to allow migrants in over recent days was an exception and that the EU’s “Dublin rules” requiring asylum seekers to be processed in the first country they arrive in remained valid.
Mr Faymann issued his statement after speaking by phone with German Chancellor Angela Merkel and Hungarian Prime Minister Viktor Orban on Sunday.
“We have always said this is an emergency situation in which we must act quickly and humanely,” the Austrian chancellor said.
“We have helped more than 12,000 people in an acute situation. Now we have to move step-by-step away from emergency measures towards normality,” he added.
Reuters news agency quotes an unnamed Austrian official as saying the change meant Austria would eventually restore spot checks on those entering the country, as it had before the weekend.
The crisis took a dramatic turn on Friday, when Hungary removed restrictions on transit and helped migrants reach the Austrian border.
On Saturday, up to 10,000 people travelled by bus, train and on foot to Vienna, with many continuing to Munich and other German cities.
Thousands more were allowed to travel from Hungary to Austria and Germany on Sunday.
The migrants had travelled north through the Balkans – Greece, Macedonia and Serbia – before arriving at Hungary’s southern border.
Germany expects to take in 800,000 people this year. Syrians are the largest group travelling, followed by Afghans and Eritreans.
Although Germany has reaffirmed that the Dublin rules on processing asylum requests are still in force, last month it waived the rule for people from Syria, allowing them to register in Germany regardless of where they first entered the EU.
On Sunday Hungarian authorities opened a new camp for migrants who have continued to arrive in the southern village of Roszke near the southern border with Serbia.
It also reaffirmed that while it had temporarily relaxed restrictions on the transit of asylum seekers, it was pressing ahead with plans to tighten border controls and could send troops to its southern frontier if parliament agreed.
A border fence is due to completed by 15 September.
Also on Sunday, a group of cars driven by German and Austrian activists travelled to Budapest to pick up migrants and distribute food.
One of the Austrian activists taking part, Angelika Neuwirth, told the BBC: “I think this is my duty. I’m a mum, I’m a woman from Austria and I can’t close my eyes anymore.”