This research work attempts to appraise the impacts of inter-agency cooperation on national security, there is no doubt that maintaining internal security in any country is a collective responsibility and the need for synergy among these distinct security bodies cannot be overemphasized. After capturing a link between inter-agency cooperation and national security based on different levels, critical problems fundamentally as to aggregate the different perspectives to the complexities of internal security operations in Nigeria was explored, relevant literal contributions from scholars were presented while asserting that inter-agency cooperation has never been embraced in Nigeria as a results of inter-agency friction and quest for superiority among them, an effective security operation is recognized as an agent of progressive national security and development in all countries of the world, leadership and management of security institution should be re-assessed to be overly supportive in strengthening national security, this investigation made use of secondary sources for data and information from national tabloids, books, internet sources among others. At the end of the analysis, it was proffered that periodic performance evaluation should be conducted for assessing their impact assessments while regulatory interference in their operations should be strategic as it is expected that embracing structural reforms is one of the major ways of improving the quality of internal security operations in Nigeria