From October 1941, Burnett had a strained working relationship with Arthur Drakeford, the Australian Labor Party's minister for air who had just then been appointed.
Burnett and Drakeford frequently clashed and when in early 1942 Burnett proposed sweeping organizational changes, including the abolition of the Australian Air Board, a breaking point was reached.
 It had also been widely argued that Burnett's focus on the European theatre resulted in the RAAF lacking sufficient defensive strength and by 1942 the threat of invasion by Japan was growing.
Burnett was replaced in May 1942 by an Australian, Air Vice Marshal George Jones, who succeeded to the position despite Burnett's lobbying for his deputy, Air Vice Marshal William Bostock, to take over.

Burnett retired from the RAF shortly after his return to Britain, but in 1943 he worked full-time in the RAF's cadet organisation, the Air Training Corps, as the commandant of the ATC's Central Command.
In this role, Burnett was responsible for ATC squadrons in Hertfordshire, Middlesex, Buckinghamshire, Oxfordshire, Berkshire and Bedfordshire.
 By 1945 Burnett remained as commandant but his health was declining and on 9 April 1945 he died of a coronary thrombosis at the Princess Mary Hospital at RAF Halton.
Charles Burnett was survived by his wife and four daughters.
From October 1941, Burnett had a strained working relationship with Arthur Drakeford, the Australian Labor Party's minister for air who had just then been appointed. Burnett and Drakeford frequently clashed and when in early 1942 Burnett proposed sweeping organizational changes, including the abolition of the Australian Air Board, a breaking point was reached.  It had also been widely argued that Burnett's focus on the European theatre resulted in the RAAF lacking sufficient defensive strength and by 1942 the threat of invasion by Japan was growing. Burnett was replaced in May 1942 by an Australian, Air Vice Marshal George Jones, who succeeded to the position despite Burnett's lobbying for his deputy, Air Vice Marshal William Bostock, to take over.
Burnett retired from the RAF shortly after his return to Britain, but in 1943 he worked full-time in the RAF's cadet organisation, the Air Training Corps, as the commandant of the ATC's Central Command. In this role, Burnett was responsible for ATC squadrons in Hertfordshire, Middlesex, Buckinghamshire, Oxfordshire, Berkshire and Bedfordshire.  By 1945 Burnett remained as commandant but his health was declining and on 9 April 1945 he died of a coronary thrombosis at the Princess Mary Hospital at RAF Halton. Charles Burnett was survived by his wife and four daughters.
Charles Burnett (RAF officer)