Efficient funds management is critical to the success of tertiary institutions especially in low income countries such as Nigeria where funding of education is abysmal. While available studies investigated cost elasticity on private demand for education in Nigeria, educational policy reform and university funding requirement, the cost centres and the relative cost control measures in Nigeria universities has not been fully explored. Means of cost savings in universities were explored in order to strike a balance between lack, insufficiency and bad management of resources. A survey research was conducted to examine the cost control measures and their ability to enhance funds management in Nigerian universities drawn across the six geopolitical zones of the country estimated under administration, finance and operations. The analyses revealed the weaknesses in the cost centres and shows that a strong positive and significant relationship exist between funds management and university administration, operation and finances with R Square 0.7019. There is a need for streamlined decision making process, greater attention to research and entrenchment of internal control mechanisms in all levels of management. Universities should be more innovative, result driven, and also de-emphasise increase in school enrolment through skills acquisition and training to create alternative jobs and drive the economy.