The Agency is managed by an Executive Director whose tasks and responsibilities are defined in Article 22 of Regulation (EUC) No 2025/2343. The Executive Director is supported by four departments and an Executive Office unit.

Currently, the Agency has 11 units, 10 of which come under these 4 departments:

Department 1: Sustainability & Technical Assistance

(Sustainability; Visits & Inspections,Human Element; Capacity Building)

Department 2: Safety, Security & Surveillance

(Safety & security; Surveillance)

Department 3: Digital Services

(Integrated Maritime Traffic Services; Maritime Digital Solutions; Horizontal Digital Services)

Department 4: Corporate Services

(Human Resources; Legal, Finance & Facilities)