Police in the state of Burgenland say they found the puppies in the trunk and back seat of the 33-year-old Romanian's car during a routine check on Wednesday.
They said the puppies were French and English bulldogs, Yorkshire terriers, and chihuahuas.
The driver told police he was a professional dog breeder and handed officers 24 European Union pet passports, which turned out to contain forged data.
A vet who examined the puppies said they were about six weeks old and hadn't been microchipped. According to European animal welfare regulations, a puppy should only separated from its mother at eight weeks of age.
Officials suspect the Romanian puppies were to be microchipped in France, so that they could be sold as French-born animals for a higher price. The driver could now face animal cruelty charges.
The puppies are being cared for at an animal welfare centre in Burgenland and will be in quarantine for the next few weeks to ensure that they don't have any viral diseases such as distemper. Animals who have been confiscated from illegal breeders are usually cared for in shelters for eight weeks before being offered for adoption.