"Today is a dark day... This tragedy affects us all deeply," Interior Minister Johanna Mikl-Leitner said at a press conference.
The vehicle, bearing Hungarian number plates, was found in an emergency lane off the highway near the border with Hungary, police spokesman Hans Peter Doskozil said alongside the minister.
Hungary said the dead appeared to be victims of a people-trafficking operation and that it would join the Austrian investigation into the tragedy.
A spokesman for Hungarian Prime Minister Viktor Orban said the driver was Romanian, according to information received from Austrian police.
It is thought that the truck -- bearing the markings of Slovakian poultry firm Hyza -- had been parked in the area since Wednesday.
"Human traffickers are criminals. Anyone still thinking that they're kind helpers cannot be helped," the minister said.
Forensics teams at the scene said it would take several days to secure evidence.
"We cannot confirm yet how they died," Doskozil added.
- 'Zero tolerance' -
Mikl-Leitner announced that 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 were meeting in Vienna to discuss how to tackle together the biggest migration crisis to hit Europe since World War II.
"We were all shaken by the horrible news that up to 50 people died... these were people coming to seek safety," Merkel said in Vienna.
"This is a warning to work to resolve this problem and show solidarity."
Orban's chief of staff Janos Lazar said Austrian and Hungarian police "will work closely together to take the necessary steps to investigate what happened, and apprehend those responsible".
"It appears that the victims were illegal migrants in a human trafficking operation."
The Austrian tragedy comes after at least 55 dead bodies were discovered Wednesday on three overcrowded migrant boats in the Mediterranean.
More than 2,300 migrants have died at sea this year during attempts to reach Europe, almost invariably on overcrowded boats chartered by people smugglers
"Just another terrible incident, illustrating the urgent need for quick and determined common action," tweeted the EU commissioner for enlargement Johannes Hahn after the Austrian find.
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.