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The Fishery Protection Squadron is the oldest front line squadron in the Royal Navy. With a small headquarters staff based in Portsmouth Naval Base, the Squadron comprises 4 River Class Offshore Patrol Vessels, 1 Castle Class Offshore Patrol Vessel and up to 4 Hunt Class Mine Counter Measures Vessels. The primary task of the Royal Navy, in its role of patrolling UK's Extended Fisheries Zone, is its involvement in the highly emotive and politically sensitive UK and European fishing industry.

The Ministry of Defence maintains a formal agreement with DEFRA and through them the Marine and Fisheries Agency for the provision of Fishery Protection in English, Welsh and Northern Irish waters by the Royal Navy Fishery Protection Squadron. Legislation permits RN Boarding Officers (BOs) to conduct inspections of all British and foreign registered fishing vessels (FVs) operating within these waters and also permits the inspection of British registered fishing vessels in international waters.

In the 2005/06 contract year, the Squadron provided 855 patrol days, conducted 1246 boardings, issued 68 written warnings and 172 verbal re-briefs and detained 19 fishing vessels. Operating from both the River Class and Hunt MCMVs, BOs conduct a range of operations, both by day and night, to conduct routine inspections.