The Commander of the Second Naval Zone aims to ensure the security and defense territorial within the assigned area, with joint operations with the Forces of Air and Earth, in case of internal or external threat, ensuring the successful achievement of the objectives of the General Operations Command Pacific. This was demonstrated during the 90 to face the subversive movements, by conducting campaigns that shook the ties between the Navy and the civilian population.
By DS No. 1 of January 10, 1962, the five naval zones, manner consistent with the territorial divisions established by the Army and Air Force are based. Thus the Commander of the II Naval Zone was created, to which they were assigned, within its territorial domain, the departments of Ancash, Huanuco, Pasco, Lima, Junin, Huancavelica, Ica, Ayacucho, and the Loreto province of Coronel Portillo. Subsequently, the latter became part of the Fourth Naval Zone.
Since its founding, the headquarters of the Commander of the Second Naval Zone is located in the Callao Naval Base, Callao.
Another function, especially in peacetime, is to enhance the institutional presence of the Naval Forces in the departments within their domain, working with the population through outreach programs, relief in case of natural disasters, and civic actions designed to generate maritime awareness and national identity.