Security challenges have threatened the unity and stability of Nigeria nation. Since there is a strong link between governance and national security. Thus, the paper examined interagency collaboration and national security challenges in Nigeria and showed clearly that there is the need for interagency collaboration amongst security agency in order to ameliorate national security challenges. Also, good governance to maintain peace and security. This is because lack of collaboration amongst security agency and bad governance threatens the security of the nation. This will makes people to lose confidence security agency and the political leaders. Thus, the federal and state as well as the local governments must develop and implement comprehensive plans to tackle not only physical security but also the grievances that fuel the insurgency. This will help to build a Nigeria where people can sleep with their two eye close and where the Hausa's, Igbo's and Yoruba's can live together harmoniously.