Not long after returning to the Netherlands from Paris, Thung was appointed as a phytopathologist at the Proefstation Vorsten landsche Tabak (Research Station for Vorstenlanden Tobacco) in Klaten, Central Java. He started work there in 1929. His research on plant diseases on tobacco plantations focused on disease control and prevention.

This period was incredibly important for Thung. He had the opportunity to engage in a combination of applied and in-depth research, conducting many experiments himself, while also closely following international research in the field. This led him to develop several theories, which are now considered established scientific facts, but were completely novel at the time.