Coming under the operational authority of Allied Air Forces Headquarters in the South West Pacific Area, RAAF Command exercised control of its units through geographically based area commands in Australia and, later, New Guinea, as well as large mobile formations including the Australian First Tactical Air Force.

Allied Air Forces (AAF) Headquarters was established under General Douglas Macarthur's South West Pacific Area (SWPA) command on 20 April 1942.

[2] On 3 September 1942, the new AAF commander, Major General George Kenney, formed the bulk of his USAAF squadrons into the Fifth Air Force.

[3][4][5] RAAF Command was charged with defending Australia, except in the north-east, protecting the sea lanes to New Guinea, and conducting operations against Japanese shipping, airfields and other installations in the Dutch East Indies.

[10] Despite the Australian Chiefs of Staff Committee recommending "unified operational and administrative control" of the Air Force, the division of command was permitted to continue, and was a source of "acute personal tension" between the RAAF's two most senior officers for the remainder of the war.

9 Group, as well as responsibility for the Port Moresby and Milne Bay sectors; South-Eastern New Guinea thus effectively became an extension of Australia for the purposes of RAAF Command's sphere of operations.

[24][25] Bostock expressed to Kenney his desire that "1st Tactical Air Force should continue to be employed as a forward offensive formation rather than in a garrison role".

1 TAF fighter pilots, dissatisfied with the ground attack and 'mopping up' roles assigned to them, had deteriorated to such an extent that eight senior officers attempted to resign their commissions in an incident known as the "Morotai Mutiny".

His aim, in concert with that of Kenney and I Corps commander Lieutenant General Leslie Morshead, was to deliver the heaviest aerial bombardment possible against enemy targets, to enable Australian assault forces to land with minimal casualties.

[6] With the end of the Pacific War in August 1945, SWPA was dissolved and Air Force Headquarters in Melbourne assumed full control of RAAF Command.

[31] The formation was disbanded on 2 September 1945, the same day that Bostock, along with Jones, represented the RAAF at the Japanese surrender aboard USS Missouri.