We aimed to document how health service providers in the Torres Strait Island region of northern Australia respond to chronic hepatitis B, and to identify priorities for the effective clinical management of the infection. Semi-structured qualitative interviews with 61 health service providers were conducted in 2011 in the Torres Strait and north Queensland region to explore issues affecting chronic hepatitis B management. Two critical issues were identified affecting the health service response to chronic hepatitis B: (i) the absence of a systems-based approach to clinically managing the infection; and (ii) variable knowledge about the infection by the health workforce. Other issues identified were competing and more urgent health priorities, the silent nature of chronic hepatitis B infection at an individual and systems level, inadequate resources and the transient health workforce. While people living in the Torres Strait region are screened, diagnosed and informed that they are infected with chronic hepatitis B, there is an ad hoc approach to its clinical management. An effective and coordinated public health response to this infection in remote and isolated Australian Indigenous communities needs to be developed and resourced. Critical elements of this response will include the development of clinical guidelines and workforce development.