Within the Directors office, the EU and Multilateral Affairs unit coordinates MEPA deliverables with an EU and Multilateral content, including co-ordination of projects financed under internationally funded instruments where MEPA is a beneficiary or service provider, and improving the environmental performance of internationally funded programmes, co ordinating input to Maltas position on EU environment pipeline Acquis and policy, and on EU obligations where MEPA has competence, co-ordination of Multilateral Environmental Agreements (MEAs) where MEPA officers are focal points, and co-ordination of overseas missions by MEPA officials to maximize business value.

UNIT A  is responsible for the environmental permitting and compliance auditing of industrial and waste management installations. The unit manages the areas of IPPC, E-PRTR, VOCs, SMEs, Better Regulation, IMPEL and UWWT; unit A  in terms of development of legislation, contributing to the development of EU legislation, provision of guidance to industry on Best Available Techniques, Emissions limits and the development of better regulation initiatives.

UNIT B (Environmental Assessment Unit) coordinates the Environment Protection Directorate's assessment of development projects and the EPD's role on related matters. In particular, the unit manages: the Environmental Impact Assessment (EIA) process, the Appropriate Assessment (AA) process, and the EPD’s coordinated technical assessment of environmentally-relevant development proposals (EPD consultations – EPDC). Among other related functions, the unit is also the EPD's primary liaison with the Planning Directorate, with the HAC Natural Heritage Panel (NHAC), and with the SEA Audit Team, and also represents environmental interests in planning-related for a and in the formulation of environmentally-relevant legislation, policy and operating procedures.

UNIT C coordinates activities, policy and strategies related to MEPA's response in the areas of ecosystems management, nature protection, GMOs and biosafety. This includes, amongst others, issues related to the EC Habitats Directive and the Natura 2000 Network of Protected Areas, the National Biodiversity Strategy and Action Plan (NBSAP), terrestrial and marine protected areas, habitat and species protection and management, nature permitting applications and processes (including CITES) and the implementation and follow-up of EU-funded projects related to biodiversity and nature protection.

UNIT D coordinates MEPA input in the following policy areas: air quality, waste management, radiation, noise and soil. The work of Unit D also includes the administration of transfrontier shipment of waste, registration of packaging and WEEE producers and the management of the air quality monitoring network.

UNIT E co-ordinates MEPA input on the following policy areas: climate change, energy, water, marine strategy and coastal zone management. Unit E is also responsible for administering the national Emissions Trading Scheme and co-ordinates the EPD input on SEVES.

The Policy Coordination Unit was set up to improve coordination between policymaking processes across the Authority. The Unit is also responsible for a number of cross-cutting dossiers such as sustainable development and environmental health. In addition, the Unit is responsible for coordinating the regular preparation of state of the environment reports and indicators.