Cooperation among security agencies is vital and of paramount importance to national security. Loose or poorly managed border posts particularly when there is no harmonious relationship among security agencies hinders effective discharge of Custom duties and negatively affect the operation success of other agencies. Evidences abound of disunity among the army, Police, Immigration and other security agencies in Nigeria while criminal elements largely exploit the cracks to conduct their illegal businesses thereby constituting national security and lead to short fall in revenue generation. This motivated the study to examine factors occasioning rift among security agencies operating along Nigeria/Benin Republic border posts and implication on national security. The paper adopted descriptive research design while the population comprised of security agencies. Secondary data sources relevant text books, journals, Internet materials and documentary evidences were relied upon. It is found that inherent lack of cooperation among security agencies was due to competition over which agency is superior and legally charged with the responsibility to perform specific function as well as greed. It recommends that inter-agency collaboration must be encouraged while there must be stiff penalty for the perpetrator of inter-agency violence, the scope of operation of each of the agencies must be adhere to and the need to minimize excessive security build up along the border line in Nigeria like in other West African nations.