Decisions of the Commission on all matters of substance are by consensus. Whether a matter is one of the substance is treated as a matter of substance. Decisions on other matters are by simple majority of the Parties present (Article 17). There is a limited procedure for notification of non-acceptance of the decision, as a last resort (Article 24). SEAFO uses dispute settlement procedures established by the UNCLOS and UNFSA. Settlement of disputes is by negotiation, inquiry, mediation, conciliation, arbitration, judicial settlement or other peaceful means (Article 24). Technical disputes may be referred to an ad hoc panel of experts established by the Commission. The Commission embraces cooperation with other regional fisheries management organisations to strengthen global high seas fishery governance in general and to sharing of information, such as IUU fishing activities. SEAFO is represented at annual meetings of CCAMLR, ICCAT, NAFO and NEAFC as an observer, and there is close working relationship with other agencies, including FAO.

One of the challenges facing the Commission includes IUU fishing whose nature and extent in the Convention area is not know. A Conservation Measure 09/07 adopted by the Commission in 2005 on Port State inspection procedures of foreign fishing vessels is a first step in addressing the issue. The system of observation, inspection, compliance and enforcement (Article 16) will be considered as more information is gathered. Another challenge is to gather baseline information on fisheries and oceanography of the region and also to improve data collection and reporting. Mandatory of onboard scientific observers in all fishing vessels are recommended as from January 2006 and satellite-based VMS to monitor the fisheries started in April 2006 (Conservation Measure 07/06).

The Commission is urging States and fishing entities with “real interest” in the fisheries of the region to become Party to Convention or to fully comply with conservation and management measures adopted.