The vehicle, which contained between 20 and 50 bodies, was found in an emergency lane off the highway near the border with Hungary, police spokesman Hans Peter Doskozil said at a press conference.
"Today is a dark day... This tragedy affects us all deeply," Interior Minister Johanna Mikl-Leitner said.
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It is thought that the truck had been parked in the area since yesterday.
"We cannot confirm yet how they died," Doskozil added.
Forensics teams at the scene said it would take several days to secure evidence.
The minister announced Austria would tighten its border controls and intensify checks on international trains in the coming weeks.
She also called on the other 27 member states of the European Union to show "zero tolerance" for people smugglers.
The gruesome find comes as German Chancellor Angela Merkel and Balkan leaders are meeting in Vienna to discuss how to tackle together the biggest migration crisis to hit Europe since World War II.
They reacted with shock to the news of the dead migrants.
"Just another terrible incident, illustrating the urgent need for quick and determined common action," tweeted the EU's commissioner for enlargement, Johannes Hahn.
This year has seen record numbers of people trying to reach the EU by sea and land as they flee conflicts in Africa, Asia and the Middle East.
In Austria, the number of asylum requests rose above 28,300 between January and June alone -- as many as for the whole of 2014 -- and officials expect the total to reach 80,000 this year.
"Austria has more migrants than Italy and Greece combined... So we shouldn't pretend that only Italy and Greece are affected," Austrian Foreign Minister Sebastian Kurz said ahead of the summit.
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