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The present Fisheries Department was established in 1966. It started operations early the following year with 2 expatriate professional officers and 15 local staff. The department was then housed at the Royal Customs and Excise building at the centre of the capital Bandar Seri Begawan known at that time as Bandar Brunei. The office was moved to the Churchill Memorial Building upon its completion. The Churchill Memorial Building in addition to the Fisheries Department also housed, the Hassanal Bolkiah Aquarium with its freshwater and marine aquaria, and part of the Museums Department which included the Winston Churchill Museum. The Hassanal Bolkiah Aquarium was demolished in 1991 to make way for the Royal Regalia Exhibition and the Fisheries Department moved out of the building to a rented area at the Athirah Building Complex. The department moved to the new Ministry of Industry and Primary Resources building in March 1996.

In the initial years of its operation, the bulk of the department manpower and financial resources (approximately 60%) were directed towards managing and running the Hassanal Bolkiah Aquarium and the running of a freshwater fish farm at Kampong Tungku in the Brunei/Muara District. The rest of the manpower and financial resources were directed towards servicing the artisanal capture fisheries. The department however did recognise the importance of the marine fish resources and in 1968, a short survey was conducted in the Brunei Waters. Even though the scope of the survey was rather limited, the survey did show the presence of a moderate fish resource that can be developed and further investigation needed to be undertaken to determine the size of the resource.