The organisation's officers were seconded from police forces from England and Wales, supported by directly recruited specialist civilian and police staff members. It was headed by a director-general and had its own service authority. The first director-general was Roy Penrose, OBE QPM, and upon his retirement in 2001, William Hughes, CBE QPM became the director-general before moving on to establish the Serious Organised Crime Agency as its founding director-general. Trevor Pearce CBE QPM previously deputy director-general took over as the third director-general before becoming an executive director and later director-general of the Serious Organised Crime Agency.
The NCS headquarters was at Pimlico in London, with three Regional Operational Command Units: Northern, Eastern, and Western with an extensive residential property estate plus other premises. Other units were the Financial OCU, the Paedophilia Unit, the National Hi-Tech Crime Unit, and the Immigration Crime Team. The NCS consisted of 1,656 full-time personnel, including 5 Directors, 1,169 seconded police officers, and 280 civilian police staff.