This paper offers an in-depth analysis of efficiency and productivity changes using the Hicks-Moorsteen total factor productivity index, in the context of higher education institutions. Unlike the Malmquist method, this approach makes no assumptions about firms' returns to scale conditions. We assume that the production technology exhibits variable returns to scale, which is more plausible than the constant returns to scale assumption, because universities usually operate at suboptimal scales. Three major groupings of Malaysian public universities are used in our case study: research, comprehensive, and focused universities. The results show that technical efficiency has improved after the 2007 National Higher Education Strategic Plan within all the three university groupings.