Some were on the verge of collapse and one woman had to be resuscitated by police.
"The van came directly from the Hungarian-Serbian border and had been on the road for six hours," police spokesman Johann Baumschlager told the Kronen Zeitung newspaper.
He said that a police patrol became suspicious of the yellow van when they spotted it at 6:00am as it was obviously overloaded, and travelling slowly.
When they told the Bulgarian driver to open the back doors they found the migrants crammed into an airless space of eight square metres. The group consisted of 24 men, 12 women and 18 children. They told police that one woman had fainted in Hungary due to lack of oxygen - but the smugglers threw a bucket of water over her and then continued their journey.
They had been forced to cut holes in the rubber sealing around the doors to be able to get a little bit of air.
The driver, who said he had been paid €500 for the job, is now in police custody. Most of the migrants are asylum seekers from Iraq, Syria and Afghanistan. Some told police that they wanted to return to Hungary.