This study appraised the implementers' perspective of the program's existing administrative and management; coordination and collaboration; and financing and accountability capacities to deliver its malaria prevention and control mandate. The instrument used was a structured interviewer-administered questionnaire adapted from an already existing National Malaria Programme's Capacity Assessment tool. Being a widely used open-source program tool, a pretest was done to ascertain its suitability and applicability to the study context and for field assistants to gain familiarity with it. The total population sampling method was used due to the small size of the target population. The target population/sample size was therefore 137, comprising the State Malaria Technical Working Group members, key officers of Cross River State Malaria Elimination Program (CRSMEP), and the Local Government Areas (LGA) Malaria implementing teams. It was a descriptive cross-sectional study. Each element per section of the questionnaire was weighted using the Likert scale and calculated using simple percentages. Research results showed that the malaria program at the State and LGA level have adequate administrative and management capacity with confirmation by 64 and 82.1% of respondents respectively. 80% of respondents confirmed average coordination and collaboration capacity at the State level while 50% of respondents at the LGA level confirmed that the program has adequate coordination and collaboration capacity. For financing and accountability capacity, 36% of respondents affirmed that there is average capacity at the State level while 37.5% confirmed that there is no capacity at LGA level. The study revealed the program's capacity gaps at State and LGA in the 3 aforementioned key areas. Therefore, interventions to address the capacity gaps are training/re-training of program staff and health workers on program management, administration, and finance, establishing performance management and accountability mechanisms, conducting evidence-based advocacy visits to policymakers for prioritizing allocating and releasing funds for malaria control activities, especially for intervention areas that are not supported by donor/partner organizations.