The number of dead could be as high as 50, police say. Their bodies had started to decompose.
The truck has been moved to an undisclosed location for detailed examination.
The shocking find comes as a summit focusing on migration takes place in the Austrian capital, Vienna.
Tens of thousands of migrants from conflict-hit states in the Middle East and Africa have been trying to make their way to Europe.
Austria’s Chancellor Werner Faymann said the tragedy showed once again “how necessary it is to save lives by combating criminals and people traffickers”.
The vehicle – a refrigerated truck with Hungarian license plates – was parked off the A4 highway between Parndorf and Neusiedl am See, according to Burgenland police chief Hans Peter Doskozil.
Officers had found at least 20 bodies inside the truck, but there could be 30, 40 or even 50 inside, he told Austrian TV.
The truck was found late on Thursday morning, August 27, but had been there since at least August 26, Peter Doskozil said.
The victims had been dead for some time.
At 15:30 local time the truck was towed away, and was due to be taken to a hall in the local area for further examination, Austrian media report.
Only there would the truck be opened and the recovery of the bodies begin, the authorities said.
The truck bears the logo of a Slovakian poultry company, Hyza, which said in a statement that the vehicle no longer belonged to the firm – but the new owners had not removed the branding.
Hungarian police are working with Austrian police on the investigation, a spokesman for the Hungarian prime minister said.
Hungary had been informed that the driver was Romanian, the spokesman said.
In Vienna, Serbia and Macedonia have told the summit on migration that EU must come up with an action plan to respond to the influx of migrants into Europe.
Austria has complained that the EU has failed to address the problem of people entering via the Western Balkans.
German Chancellor Angela Merkel said today’s find “reminds us to tackle the issue of migration with European spirit and find solutions”.
A record number of 107,500 migrants crossed the EU’s borders last month and on August 26 police counted more than 3,000 crossing into Serbia.
Meanwhile migrants are continuing to die as they try to reach Europe via the central Mediterranean route. The bodies of at least 51 people were found on August 26 in the hold of a stricken ship off the coast of Libya.
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