The emergency measures for asylum seekers will be removed “step by step”, the chancellor added.
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 heading, 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 rules requiring asylum seekers to be processed in the first country they arrived in remained valid.
Chancellor Werner Faymann issued his statement after speaking by phone with German Chancellor Angela Merkel and Hungarian PM Viktor Orban on September 6.
“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.
The change means that Austria will restore spot checks on those entering the country, as it had before the weekend.
On September 6, a group of cars driven by German and Austrian activists travelled to Hungary to pick up migrants and distribute food.
Hungarian police said anyone taking people across the border was breaking the law on people smuggling – although the activists were able to collect migrants without being stopped.
The crisis took a dramatic turn on September 4, when Hungary removed restrictions on transit and helped migrants reach the Austrian border.
On September 5, about 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 September 6.
The migrants had travelled north through the Balkans – Greece, Macedonia and Serbia – before arriving at Hungary’s southern border.
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