Ethnic minority tensions and agitations in Nigeria are important features of the on-going struggle to resolve the “national question” through convening the Sovereign National Conference, all in a bid to dialogue and negotiate a true federal system that incorporates and accommodate the minorities within the federal system. This paper suggests that the minority issue in Nigeria is deeply rooted in the complex triad of pre-colonial, colonial and post-colonial historical and structural processes that have foisted and institutionalized the oppressive hegemony of the country’s three major ethnics over the minorities. To further illuminate this perspective, we have adopted Edward Azar’s Protracted Social Conflict (PSC) theory as both a theoretical and an explanatory tool. The minorities’ response to this inequality has move along the trajectory of protest, agitation to establishment of militias groups to argument for self-determination and now a call for negotiation. The official response has been redistributive (minor or token changes in the revenue sharing formula), reorganization (creation of more states/local governments), and repressive or regulative (leading to ban of political parties and other cultural organizations of the minorities). These intimidatory and repressive responses have only made more strident the minorities’ call for a negotiated federal system while questioning the legitimacy of the present systemic arrangement. It is in this regard that the present administration has decided to convene a national dialogue or national conference to discuss some of the issues involved. However, the different and sometimes conflicting agenda being floated as core issues by different groups and affiliations for discussion may inhibit or nullify the entire negotiation process and outcomes