Headquartered at Townsville, Queensland, North-Eastern Area Command's responsibilities included air defence, aerial reconnaissance and protection of the sea lanes within its territory.

[1][4] Air Commodore Frank Lukis, formerly in charge of Northern Area, was NEA's inaugural AOC, taking responsibility for RAAF operations against the Japanese in New Guinea, New Britain and surrounding islands.

[7] On 20 January 1942, over 100 Japanese aircraft attacked Rabaul, destroying or badly damaging six CAC Wirraways and killing or wounding eleven crewmen of No.

Ignoring a further message from headquarters to abandon his squadron and escape in a Lockheed Hudson bomber, Lerew began evacuating staff to Port Moresby, New Guinea, on 22 January.

33 Squadron, operating ex-Qantas Short Empire flying boats and several smaller transports, was raised in NEA on 19 February 1942.

At one point NEA headquarters gave Jackson permission to withdraw but he refused, and the squadron was eventually credited with destroying thirty-five Japanese aircraft in the air and on the ground, securing Port Moresby until relieved by the 35th and 36th Squadrons of the United States Army Air Forces (USAAF), operating P-39 Airacobras.

According to the official history of the RAAF, though "more a diplomatic gesture than a practical method of war organisation", it gave personnel from the two services the opportunity to quickly become acclimatised to each other and "in North-Eastern Area, as an example, the atmosphere was happy and the staff extremely cooperative".

Located on Green Street, Townsville, at the base of Castle Hill, it was topped with a suburban house to mislead enemy aircraft.

[27] The Japanese raided Townsville four times between 25 and 31 July; most bombs fell in the sea or the hills causing only one casualty, an injured child.

[28] NEA's boundaries were fine-tuned on 19 August: a portion of Queensland within the Barkly Tableland and the Haslingden and Heywood districts was assigned to the control of North-Western Area.

76 Squadron, deployed north from Townsville and also flying Kittyhawks, played what senior Australian Army commanders described as the "decisive" role in the Battle of Milne Bay in New Guinea during August and September 1942.

9 (Operational) Group was formed at Port Moresby as a mobile strike force to move forward with Allied advances in the Pacific, in contrast to the static, defensive nature of the area commands.

[30] September 1942 also saw the formation of RAAF Command, led by Air Vice Marshal Bill Bostock, to oversee the majority of Australian flying units in the SWPA.

[36][37] Bostock exercised control of air operations through the area commands, although RAAF Headquarters continued to hold administrative authority over all Australian units.

[38] He personally coordinated operations when they involved more than one area command, for instance when the fighter squadrons of both NWA and NEA were required to repulse a major attack.

12 Squadron (Vultee Vengeance dive bombers), the wing was responsible for Torres Strait's air defence, as well as offensive operations against infrastructure and shipping in Dutch New Guinea.

75 Wing headquarters moved from Horn Island to Higgins Field, where it was soon joined by other units under its control, Nos.

7 and 23 Squadrons; the latter operated Vengeances until being declared non-operational in June, before re-equipping with B-24 Liberators for duty in North-Western Area.

[44] Cobby served as AOC NEA until November 1943, handing over to Air Commodore John Summers, who held command for the remainder of the war.

76 Wing headquarters, formed at Townsville in January and subsequently based at Cairns, was transferred to Darwin, Northern Territory.

[60] The Air Force shrank dramatically as personnel were demobilised and units disbanded; most of the RAAF's bases and aircraft employed in operations after the war were situated within Eastern Area's sphere of control in New South Wales and southern Queensland.

10 Squadron was based at Townsville from March that year, operating Avro Lincolns over the Pacific and Australia's northern approaches in the maritime reconnaissance and search-and-rescue roles.

[72][73] As of 2009, the former NEA operational headquarters in Building 81, Green Street, housed Townsville's State Emergency Service group.