FISHREG's research and policy support work is organized as two main activity clusters, "Fisheries Management" and "Fisheries Economics". In addition, FISHREG is contributing to the fight against IUU fishing and to selected initiatives of the EU Integrated Maritime Policy (IMP).
Under an agreement with Directorate General (DG) Maritime Affairs and Fisheries (MARE) of the Commission, FISHREG coordinates the scientific advice process of the Commission's own Scientific, Technical and Economic Committee for Fisheries (STECF). FISHREG provides the STECF Secretariat and offers scientific input to STECF in a number of areas. STECF Subgroups deal with research needs, economic affairs, stock reviews, Mediterranean and Black Sea stocks, management objectives and strategies, and the balance between resources and exploitation. For more information see STECF web site.
FISHREG collects and maintains fisheries data reported by EU Member States in the framework of the Data Collection Framework (DCF) - previously the Data Collection Regulation (DCR). Several times a year, following formal data calls by the Commission, national correspondents upload their data using a dedicated web site run by FISHREG. There are at least four different types of data gathered by FISHREG: biological, economic, fishing effort and discards. The focus of the data calls and the variables can change from year to year. For more information see Data Collection web site. The datasets gathered by FISHREG are first checked for compliance and quality, and then normally placed at the disposal of independent experts participating in Working Groups of the STECF in charge of scientific advice. Challenges addressed by JRC in data collection include the development of quality assurance procedures, common codifications, and aggregation for analysis and assessments.
FISHREG annually collects economic data on the EU fishing fleet and fish processing sector. In collaboration with DG MARE, it issues the Annual Economic Report (AER) on the European Fishing Fleet. Independent experts are invited in the framework of STECF to provide the material for the national chapters of the AER. FISHREG also edits and co-authors the Annual Economic Report on EU fish processing sector. Finally, to address the problem of rising fuel costs, FISHREG gathers information on best practices for energy efficiency in fisheries and publishes it through a dedicated web site, Energy Efficiency in Fisheries.
Work in the fight against IUU fishing includes research into advanced techniques for product traceability based on forensic genetics and chemistry. In addition, FISHREG does research in the spatial and temporal variability of pelagic fish habitats.
FISHREG follows closely developments in the framework of the Integrated Maritime Policy (IMP). It maintains an advisory role for action EMODNET by DG MARE on common data infrastructures for industrial, research or policy purposes. In addition, FISHREG, as a thematic assembly center for fisheries data, is required to address a number of challenges to improve access to high quality data for the wider research community (see also Marine Knowledge). These challenges include the lack of regional databases, the slow response to calls for data for management advice, wrong formats in the data submitted, or the lack of standards for software or codification in the Member States.  Finally, FISHREG has an interest in contributing to the future development of the public web-based European Atlas of the Seas (MARATLAS project of DG MARE), for example, using selected fisheries data collected by FISHREG.
FISHREG maintains a strong interest in European Marine and Maritime research and regularly considers opportunities for participation in relevant collaborative research consortia.
Before 2010 FISHREG spent a large proportion of its overall effort in support of fisheries enforcement. In fact, JRC began work in fisheries in 1999 with research on the potential use of Synthetic Aperture Radar (SAR) to detect fishing vessels from satellites. This research and project IMPAST that folowed it, have been instrumental in the development of Vessel Detection System (VDS) technology, a new control tool independent of VMS. About 7 years later, VDS became part of EU control regulations. During this period, JRC validated and refined VDS through contributions to numerous control campaigns in EU seas, in collaboration with national Fisheries Monitoring Centres (FMCs), Commission officials in charge of fisheries control, and, in the last few years, the CFCA. FISHREG provided satellite-based vessel detection, most of it in near-real-time, to target controls and understand fishing patterns (VDS leaflet).
FISHREG also advised the Commission on exchange formats and data infrastructures to share data with Member States in support of the Electronic Reporting Systems (ERS) Regulation (providing for e-sales notes and e-logbooks). Previous to that, JRC was scientific coordinator of project SHEEL, a seminal piece of work on electronic logbooks. In 2010, work in fisheries enforcement included the transfer of VDS technology to the Community Fisheries Control Agency (CFCA) and Commission support for the implementation of ERS.