In 1965 Vágner took over as the director of the zoo in Dvůr Králové nad Labem, then known as the East Bohemian Zoological Garden (Czech: Východočeská zoologická zahrada).
[citation needed] An enthusiast of Africa, Vágner developed the previously unknown zoo into Europe's largest collection of African ungulates.
While some of the imported animals travelled further to other zoos across Europe, most remained in Dvůr Králové, forming some of the largest breeding herds of antelopes, zebras, giraffes, buffalos and rhinos outside of Africa.
Vágner's idea of exhibiting large herds of African ungulates at the zoo was based on the concept of panoramic enclosures, developed by Karl Hagenbeck in Hamburg.
A part of the zoo's area was landscaped panoramically, with dry moats and paths between individual grassed exhibits not visible to the spectator.
He was involved in the development of Košice Zoo in Slovakia, prepared a settlement plan of the left bank of Tana River for the Kenyan government, and created an Indian Rhino conservation scheme for India's Assam region.
Vágner was the author and co-author of nearly fifty research papers, as well as a similar number of popular articles, and appeared often on TV and radio.
Outside Czechoslovakia Vágner gave public speeches and lectures in Austria, Belgium, Denmark, France, Germany, Hungary, Italy, the Netherlands, Poland, Russia (USSR), Sweden and the United Kingdom.