After a period as a research fellow at the Australian National University's Urban Research Program, in 1998 Mees returned to the University of Melbourne to teach and research. In 2008, amid a public furore over academic independence, he was demoted by the university. Its key complaint related to public criticisms Mees had made about state government officials, although a subsequent investigation dismissed the university's complaints. By that time, however, Mees had resigned to take up an appointment at RMIT University. Promoted to associate professor in 2012, Mees researched and taught at RMIT until his death.