Issues such as financial autonomy, academic autonomy and administrative autonomy are crucial to the effective management of university education globally. For many years Nigerian universities have complained of being impeded in these areas because of the supervisory role of the National Universities Commission (NUC) which tend to encroach on their autonomy. In order to confirm this complaint and profer solution 280 university administrators and 100 university union officials from the 10 universities in the South-South Geopolitical zone of Nigeria were surveyed. An instrument known as the "National Universities Commission Supervisory Role and Effect questionnaire" was used for data collection. The chi-square statistical method was used for data analysis. The study revealed that the supervisory role of the NUC in the areas of funding, ensuring minimum academic standards, and political interference in the appointments of vice-chancellors and Governing Councils has been abused resulting in the poor management of Nigerian Universities. The paper subsequently recommended that these anomalies be eliminated through an amendment of the statute that established the NUC in order to give the universities the necessary autonomy for growth. (Contains 10 tables.)