In 1967 he became a professor at the University of Kiel at the Institute of Marine Sciences (Institut für Meereskunde Kiel), where he remained director of the Department of Fisheries Biology for the next 14 years and served as Acting Director of the institute from 1972 to 1976.
He has been interested and active in research politics throughout his career. From 1963 to 1967 he worked for UNESCO and the FAO and from 1990 to 1996 he was a member of the Wissenschaftsrat, the scientific advisory committee of Germany. He has been and is an active proponent of scientific collaboration and education initiatives in underdeveloped countries, and has advocated a more sustainable exploitation of natural resources. Hempel is the editor of the journal Polar Biology, and he has also published several books. He has had more than 70 doctoral candidates, notably Daniel Pauly. From his time spent researching oceanological topics he has managed to spend over 1000 days aboard research vessels.