In April 1991, the Secretary of State for Scotland established the fisheries protection and enforcement services as an executive agency as part of the Government's Next Steps Initiative, which sought to devolve specific activities from central Government to free-standing organisations, headed by Chief Executives accountable to Ministers.
Following devolution in Scotland, the agency transferred to the control of the Scottish Executive Environment and Rural Affairs Department (SEERAD).
In April 2009, the SFPA officially ceased to exist, with its duties being absorbed into the newly established Marine Scotland.
The SFPA was responsible for monitoring compliance and taking enforcement action, where necessary, to deter and detect illegitimate activities in the marine environment.
It housed the supporting arms of the Agency including Finance, Corporate Affairs, Human Resources, Training, Pay, Procurement and Health & Safety as well as the Prosecution & Enforcement Policy branch and the Marine Monitoring Centre (previously known as the HQ Operations).
The Marine Monitoring Centre was responsible for tasking SFPA assets, primarily FPVs and surveillance aircraft, to address the key priorities, which were determined using risk-based analysis.
From 1 June 2005, the UK Fisheries Call Centre (UKFCC), based within the MMC, has been the single point of contact for all notification or reporting requirements from fishing vessels in UK waters, working of behalf of Marine Scotland Compliance, the Marine Fisheries Agency of England and Wales (MFA), and the Department of Agriculture and Rural Development of Northern Ireland (DARNDI).
In 1994, the Agency determined that this assistance was no longer required and the Fishery Protection Squadron was moved to Portsmouth as part of the Strategic Defence Review (SDR).
From that time, all Fishery Protection operations in Scottish waters (with the exception of joint exercises[6]) were conducted by SFPA vessels.
The Marine SFI had approximately 133 staff and had projected running costs of £9,421,000 for 2008–2009The Jura-type offshore patrol vessels were 84m in length with a displacement of 2,200 tonnes.
The first vessel of the type, FPV Jura, was constructed by Ferguson Shipbuilders of Port Glasgow, joining the fleet in March 2006.
The first of the type, FPV Sulisker was launched in 1980, decommissioned late 2006 and is currently undergoing conversion to a luxury yacht in Lowestoft.
The vessel was purchased by Sea Shepherd Conservation Society in 2006 and was renamed MY Robert Hunter in memory of one of the two founding members of Greenpeace.
The Steve Irwin has become a popularly recognised ship due to the Animal Planet television programme Whale Wars which documents the work of Sea Shepherd including their use of the vessel.