Introduction: Points of Entry (PoEs), such as seaports, are critical for managing the movement of people and goods. Nevertheless, they are also significant vectors for the international spread of infectious diseases. As such, the International Health Regulations (IHR) established by the World Health Organisation are a cornerstone of global public health security, requiring countries to strengthen their preparedness and response capacities at PoEs. However, like many developing countries, Nigeria faces significant disparities in preparedness, leaving it vulnerable to emerging health threats, particularly in the post-COVID-19 era. Therefore, this study assessed the core capacities related to preparedness and response at three key Nigerian maritime PoEs: Lagos Apapa, Rivers, and Delta Port. Method: We employed a descriptive cross-sectional survey using the State Party Annual Reporting (SPAR) questionnaire to evaluate core capacity parameters, including allocated funds, training, equipment availability, inter-agency collaboration, and emergency contingency plans. Results: Findings indicate significant regional disparities, with Lagos Apapa showing relatively better preparedness than Rivers and Delta Ports, which faced considerable challenges in funding, training, and equipment availability. Specifically, Lagos Apapa port reported 75% (functional capacity in funding, while Rivers and Delta ports face minimal functional capacity, particularly in training (15.9% and 9.1%) and equipment availability (19.1% and 16.0%). Conclusion: These findings demonstrate critical gaps in Nigeria's public health infrastructure at PoEs and emphasise the need for targeted interventions to improve core capacities, contributing to ongoing efforts to strengthen public health systems at PoEs in developing nations, in alignment with the IHR.