The refugees, mostly Afghans, had been locked into the lorry for at least 12 hours, and an eight-month pregnant women had to be taken to hospital after blacking out.
Several others had also taken ill, according to public broadcaster ORF, with the migrants forced to make holes in the lorry’s sides so they could breathe.
The lorry’s driver abandoned the vehicle before police arrived.
Police spokesman Johann Baumschlager said that it was “by far the worst case of smuggling” the Lower Austrian police force had seen and that even experienced officers were shocked. The Red Cross provided the exhausted migrants with drinks and a meal of pasta.
Also on Saturday Austrian police found six Syrian families, numbering 40 people, sitting on the grass at a lay-by on another motorway, ORF also reported.
The discovery came as another 18 migrants were found stowed away on a lorry on a British motorway.
Police believe they had been carried through the Channel Tunnel from France in the back of the vehicle before being discovered 111 miles (178 kilometres) to the north on the M1 near Luton.
Police tweeted a picture of the migrants sitting on the ground next to a parked lorry loaded with cargo, apparently at a motorway service station. There were no reports of any being unwell.
A spike in the number of migrants trying to cross the Channel from France to Britain has pushed the issue to the top of the political agenda there.
Austria is on the main migrant land route into Europe, with thousands passing through the country after crossing into the European Union over the Serbia-Hungarian border.
Most are trying to reach Germany and Scandinavian countries. Only two of the migrants found in the lorry near Sankt-Pölten, west of Vienna, have asked for asylum in Austria.
Groups of migrants are stopped almost daily crossing Austria.