The operational activities of the Command include maintaining presence at sea, anti-smuggling, anti-sea robbery/piracy, anti-fishery patrol and anti–illegal bunkering. Others are, escort duties, RMAC surveillance, Falcon Eye (FE) and joint operations.  These are discussed in details:

a. Anti-Smuggling. Anti-smuggling operations are carried out within ENC AOR in fulfillment of NN constitutional role to police the nation’s territorial waters. In the ENC, most smuggling activities occur in Calabar and Akwa Ibom State waters sharing international maritime boundaries with the Cameroon, Equatorial Guinea and Sao Tome. It is worth noting that this area serves as a major hub for smuggling in the ENC AOR. Hence, NNS VICTORY and FOB IBAKA mostly conduct anti-smuggling operations to curtail such activity through which sub-standard goods are smuggled into the country. This invariably affects the positive growth of local industries producing goods that have been banned from importation by the Federal Government of Nigeria. The anti-smuggling efforts of the Command have recorded a huge success leading to the drastic reduction of smuggled goods into the country. The Command has contributed immensely to support the efforts of the Federal Government towards rice production in Nigeria

b. Anti-Illegal Bunkering/Refineries Operations. Anti-Illegal bunkering /refineries operations are one of the main operational thrust of the ENC. The operational concepts of fixed station patrol and choke point control to stem the tide of COT, illegal bunkering, illegal refinery and pipeline vandalism is yielding results. The approach ensures substantial increased presence. Additionally, the deployment of Manta boats, Modant Marine and Epenal boats has greatly contributed to the realization of this objective. Reduction in oil theft and illegal refineries in the ENC AOR is a testimony to the successes achieved so far

c. Escort Duties. Units under command are involved in providing security in form of escort and static guard duties to international oil companies and their subsidiaries. Collaboration with the PMSCs that provide security to installations and sustained escorts has enhanced security in the AOR. All PMSCs boats operating in the ENC have installed HF radio sets for a common anti-piracy reporting net as well as AIS equipment. Coordination of efforts to respond to threats or attacks has been enhanced.  There are 22 PMSCs operating within ENC AOR. Naval convoy escorts of ferry boats is also maintained for Calabar, Opobo, Bonny, and Port Harcourt River Channels with the PMSCs. 

d. Joint Operations. Units in the Command are involved in various joint operations such as Op DELTA SAFE, SKOLOMBO, THUNDER and SPARK. NNS VICTORY for instance provides naval components for Op SKOLOMBO in Cross River State, NNS JUBILEE and FOB IBAKA provides for Op THUNDER in Akwa Ibom while NNS PATHFINDER provides for Op SPARK in Rivers State. Meanwhile, all bases within ENC AOR are components of Op DELTA SAFE. The impact of the operations has resulted in the decline in crude oil theft, pipeline vandalism, illegal bunkering and by extension enhanced security within the states in realisation of the Key Priorities of the CNS Strategic Directive – 2.

e. Surveillance Capabilities. The Command employs both the RMAC and Falcon Eye facilities to monitor shipping movement. This has become a veritable source of information as it is used to vector NN vessels to investigate suspected contacts. It has also been used for tracking pirate mother vessels and vessels suspected to be involved in illegalities. Apart from the Display Centres at Calabar, there are Sensor Sites at Ibaka, Bonny and Iko.