Slovenia wants the Krainer sausage to be given special protected EU status - like Melton Mowbray pork pies, the Cornish pasty, Champagne and Parmesan.
The country insists that the speciality, made of minced pork and seasoned with garlic and pepper, originated in northern Slovenia's Kranjska region in the 19th century, meaning it should get Protected Geographical Indication status.
However, Austria claims that a cheese-filled version of the sausage, called the Kaesekrainer, was invented in their country.
Both are battling to claim ownership of the pork sausage, the BBC reports. Only a sausage made in the winning region could be called a Krainer.
The European Commission with make a ruling on the issue if the two countries can't settle the dispute in the next six months.
"To rename this beloved speciality is simply impossible. Vienna sausage stands are a trademark of the city and Kaesekrainers have to be on offer," Vienna Chamber of Commerce's Josef Bitzinger said.
"Frankfurter sausages are called Wiener Wuerstel in Germany and that is not a problem."