The Agency is managed by an Executive Director whose duties and powers are defined in Article 15 of Regulation (EC) No 1406/2002. The Executive Director is directly supported by three Heads of Department, a policy advisor, a communications advisor, an accounting officer and an internal audit capability.

Currently, the Agency has 9 units, under 3 departments:

• Department A: Corporate Services
  (Human Resources; Legal and Financial Affairs; IT and Operations Support)
  
  
• Department B: Implementation of the maritime safety and protection of marine environment acquis
  (Safety Assessments and Inspections; Ship Safety; Marine Environment, Training and Statistics)
  
  
• Department C: Operations
  (Pollution response services; Vessel traffic and reporting services; Satellite based monitoring services)