This was the first major application of this approach to hospital funding in a publicly funded health system[5] Duckett was appointed Departmental Secretary to the Australian Government Department of Human Services and Health on the recommendation of Prime Minister Paul Keating in 1994 and served in that role until the change of government following the 1996 federal election.

During this period he continued research on aspects of hospital economics and published a book on the Australian health care system.

Shortly after his appointment, the provincial government imposed a significant ($1billion) budget cut on Alberta Health Services.

On 20 November 2010, Duckett came under scrutiny for televised remarks to the media following a high-level meeting about the situation in the province's emergency rooms.

During the aired segment, Duckett refused to answer questions by reporters waiting outside the meeting room, using the excuse he was eating his cookie[9] and that another person had been designated to make comments.

[11] On 24 November 2010, following political intervention,[12] the chairman of the Alberta Health Services Board announced that, by mutual agreement, Duckett would vacate his role.

In late 2012 he joined Grattan Institute, a domestic public policy think tank based in Melbourne, as head of its Health program.