An Austrian Interior Ministry statement said it appeared that the "many bodies" found in the truck, whose number has not yet been confirmed, are refugees.
The truck was abandoned on the side of the A4 highway, which links Budapest in Hungary to the Austrian capital, Vienna, a spokesman for the Interior Ministry told CNN on Thursday.
When police opened the back of it, they found the bodies, Alexander Marakovits said. He added that he wasn't able to say how many bodies were found and that police are seeking the driver.
"These people seem to have died a while ago. It is not clear what the cause of death was, the investigation is ongoing," said the director of state police, Peter Doskozil.
The truck was left in an emergency stopping zone in the Neusiedl district of Burgenland, the Interior Ministry said.
"This horrible crime shows that we must get even tougher in the battle against people smuggling," Interior Minister Johanna Mikl-Leitner said at a news conference.
"People smugglers are criminals and not well-minded helpers. They do not care about the well-being of the refugees, they care about profit."
The Italian coast guard earlier said that 54 migrants were found dead on boats in the Mediterranean on Wednesday.
Another 3,000 men, women and children were rescued in multiple operations off the Libyan coast Wednesday, the coast guard said. They were found on vessels ranging from rubber dinghies to fishing boats.
Bodies found in boat's hull
A Swedish coast guard vessel, operating on behalf of the European Union border agency, found 51 of the migrants who lost their lives in the hull of a large fishing boat and saved 439 other people who were on board.
It's not yet confirmed what caused the deaths, but in the past, migrants trapped on the lower decks of vessels have died of asphyxiation or been poisoned by the fumes from leaking engines. The Italian coast guard initially said 50 had died.
On the same day, the Italian coast guard found three women dead in a rubber dinghy in the Mediterranean.
A number of international ships working under the EU border agency, Frontex, also took part in the rescue operations, the Italian coast guard said.
Humanitarian group Doctors Without Borders, also known as Medecins Sans Frontieres, said its own ships also carried out rescues.
One, the Argos, was headed to Italy on Wednesday evening with more than 700 people on board, it said on Twitter.
The International Organization for Migration said the number of deaths of all migrants and refugees attempting to reach Europe by sea in 2015 stood at 2,373 as of Tuesday
The death toll for the whole of 2014 was 3,281, and the IOM fears that this year's total could well surpass that, if boats carrying migrants continue to attempt the crossing in increasingly uncertain weather.
"Last year, from late August through the end of December, over 1,200 migrants died at sea," its news release said. "IOM is concerned that as summer turns to autumn and then winter, additional deaths at sea could well surpass 2,000 through the final third of this year."
The so-called central route, from North Africa to Italy and Malta, is the deadliest of three commonly used by traffickers who cram migrants onto often unseaworthy boats in a bid to reach European soil, the IOM said.
There have been 2,267 deaths on that route so far this year, the IOM said, with another 83 on the eastern route -- Turkey to Greece -- and 23 more on the western route between Africa and Spain, including the Canary Islands.
Those rescued so far this year at sea include Eritreans, Somalis, Sudanese, Sub-Saharan Africans, Syrians and Bangladeshis, the IOM said. While some are refugees fleeing conflict, others are making the perilous journey in hope of finding work.