As AOC Training Command in 1954, Murdoch headed a program to determine aircraft purchases for the RAAF; his recommendations included the C-130 Hercules transport, considered one of the most important acquisitions in the Air Force's history.

[1][2] Educated at Caulfield Grammar School, Alister entered the Royal Military College, Duntroon, in 1929, following his elder brother Ian (later a major general).

[3][4] In December 1935, Flying Officer Murdoch was selected to join an RAAF rescue mission for explorer Lincoln Ellsworth and his pilot, Herbert Hollick-Kenyon, who were presumed lost while journeying across the Antarctic.

[3] Promoted to group captain, Murdoch was appointed senior air staff officer (SASO) at Eastern Area Command, Sydney, in July 1943.

[3] In January 1944, he became SASO at North-Western Area Command, which controlled thirteen Australian, British, Dutch, and American squadrons from its headquarters in Darwin, Northern Territory.

[3][14] Murdoch planned many of the command's bombing and mining operations in the South West Pacific Theatre,[3] and was mentioned in despatches for his "distinguished service" in the role.

1 TAF) in April 1945, replacing Group Captain William Gibson after the latter's dismissal in the wake of the "Morotai Mutiny", when the threatened resignations of eight of the RAAF's leading fighter aces caused a crisis in the formation's leadership.

1 TAF's new commander, Air Commodore Frederick Scherger, Murdoch received much of the credit for the planning of the RAAF's role in Operation Oboe Six, the invasion of Labuan.

[21] One of a small coterie of officers earmarked for top positions in the post-war Air Force, he was Director of Personnel Services in 1946–47 before attending the Imperial Defence College, London, in 1948.

[3][10] In 1954, Murdoch led a mission to examine potential new fighter, bomber, transport, and training aircraft for the RAAF, following a shift in defence funding towards the Air Force.

In October 1959, Murdoch was posted to London as Head of the Australian Joint Services Staff,[3] and appointed a Companion of the Order of the Bath (CB) in the 1960 New Year Honours.

[29] He was the last of a quartet of army-trained CASs; from 1954 to 1969 inclusive, every RAAF chief—John McCauley, Scherger, Hancock, and Murdoch—had been a cadet at the Royal Military College, Duntroon, before serving with the Air Force.

Wilton's successor as CGS, Lieutenant General Sir Thomas Daly, urged Murdoch to procure specialised helicopter gunships such as the AH-1 HueyCobra for Vietnam, to support the more vulnerable troop-carrying "slicks".

[37][38] Murdoch's failure to appreciate the need for cooperation with land forces has been blamed for fostering long-running enmity between the services, which twenty years later would contribute to the government's decision to transfer the RAAF's battlefield helicopters to the Army.

[39] Murdoch also opposed sending Canberra jet bombers to Vietnam on what were later described in the official post-war history of the RAAF as "misleading" grounds that the type was unsuitable for a low-level strike and close support; their deployment went ahead in April 1967.

[41] Murdoch attended the much-anticipated official hand-over ceremony for the aircraft on 4 September 1968 at Fort Worth, Texas, with Defence Minister Sir Allen Fairhall, US dignitaries, and RAAF F-111 crews.

In late 1969, Murdoch accompanied Secretary of Defence Sir Henry Bland to the United States to gain assurance of an adequate "safe life" for the F-111's swing-wing mechanism, amid the Australian government giving serious consideration to abandoning the program.

[7][44] He was succeeded by Air Marshal Colin Hannah, whom Murdoch had earlier recommended for the position of Commander Australian Forces Vietnam (the role went to an Army officer, as had been previous practice).

[45] In 1971, Murdoch joined the board of directors of Meggitt Limited, an oilseed-crushing firm that was chaired by World War II fighter ace Nicky Barr.