Following the outbreak of the Pacific War, the PIB served in many of the Allied campaigns in New Guinea; however, due to the nature of its role its sub-units mainly operated separately, attached to larger Australian and US Army units and formations.

Enlistments in the PIB began in June 1940, with the first 63 recruits being current or former members of the RPC, a connection which allowed the unit to claim a lineage to the Armed Native Constabulary, which had been formed in the late 19th-century to police the Protectorate of British New Guinea.

Designated Lark Force, it tasks included protecting the airfields at Lakunai and Vunakanau and the seaplane base in Simpson Harbour, as well as forming an "advanced observation line" to provide early warning of Japanese movements.

Equipment provided included a waterproof cape, clasp knife and lanyard, two pairs of khaki shorts and shirts per year, two green sashes, sulus for working and sleeping, in addition to a mosquito net, blankets, plates and eating utensils, webbing, rifle, bayonet, and helmet.

[15] Australian defences in Papua remained limited and were centred on Port Moresby, consisting of approximately 1,000 only partially trained Militia from the 49th Battalion, two six-inch coastal guns, a 3.7-inch anti-aircraft battery and a few Consolidated PBY Catalina flying boats, in addition to the locally recruited PIB which was still forming, and the part-time volunteer NGVR.

Lieutenant Colonel John Scanlan considered he would need an entire brigade to defend Rabaul, yet with an invasion imminent all he could do was redeploy some of his limited force, while the remaining aircraft were withdrawn and the airfields cratered.

[23] The PIB subsequently conducted a number of small patrols from Redscar Bay to Rigo, and inland to the foot of the Owen Stanley Range, which served as an occasional relief from heavy labouring.

[26] These patrols consisted of a number of small reconnaissance parties which had been dispatched to Obu near Yule Island in the Gulf of Papua, as well as to Hisiu on the west coast, Rigo, and the Owen Stanley Range.

[41] Meanwhile, elements of the US Fifth Air Force began arriving in Port Moresby, commencing bombing operations against Japanese positions at Lae, Salamaua and Rabaul, with the PIB tasked with search and rescue for downed airmen.

[51] On the night of 21/22 July, 3,000 Japanese landed near Gona in an attempt to advance south overland through the mountains of the Owen Stanley Range to seize Port Moresby as part of a strategy of isolating Australia from the United States.

[52] With the brigades of Allen's 7th Division now reinforcing Maroubra Force, the PIB was organised into teams of stretcher bearers and was assigned the task of evacuating sick and wounded Australian soldiers back along the Kokoda Track.

[79][Note 8] After the battalion returned to Port Moresby in early 1943 the administrative requirements of the unit changed, and the headquarters was subsequently stationed at Bisiatabu, with the rifle companies in the future operating independently under different Australian or US divisions.

A patrol from 4 Platoon was able to determine its approximate position after questioning the local people, and a small group of three Papuans under Lance Corporal Bengari then infiltrated Japanese lines to confirm its location.

[109] On 11 September the elements from A Company, PIB which had remained on Charlie Hill, cautiously moved into Salamaua which they found largely destroyed, with decaying food, rubbish and Japanese corpses strewn among the ruins.

B Company, PIB under the command of Captain John Chalk, was subsequently attached to the battalion for scouting and patrolling, leaving Port Moresby on 26 June and flying to Wau, before moving to Bulolo and then down the track to the Wampit River where they established a base on 1 July.

That evening the Japanese counter-attacked the Papuan positions around the Mission, only to be driven back after heavy fighting which resulted in a number of civilian casualties after the village had been accidentally hit by stray small-arms fire.

Japanese forces were more active in the west, while the Australian positions in this area were dangerously dispersed, with a large distance between the Papuans around the 5800 feature and the 2/6th Independent Company to their left on the Solu River, with this gap considered to be vulnerable to infiltration.

[139] After midnight on 7/8 December the booby traps in front of 7 Platoon exploded as a large Japanese force estimated at approximately two companies assaulted the forward Papuan section, guided by hostile natives.

[144] Part of a Japanese attempt to push the Australians off the hills and into the Ramu Valley, the attack was followed by moves against positions held by the 2/6th Independent Company on 8 December which forced a number to be withdrawn, while other elements were cut-off.

[159] An area of tactical importance due to its dominating position and the observation it provided, D Company, 2/17th Battalion pushed past the mission, and by 25 September was 5 kilometres (3.1 mi) west before meeting resistance.

Meanwhile, in an attempt to regain Pabu the Japanese reoccupied Pino Hill, only to be forced to abandon in the face of a deliberate attack by infantry from the 2/32nd Battalion supported by four Matilda tanks, and heavy preparatory fire from the artillery, with 9 Platoon, PIB attached as scouts.

[174] Initially under the command of Lieutenant Ernest Vickery after Hitchcock went on leave in November, the company was involved in heavy contact with the Japanese retreating from Fortification Point to Sio, and then along the Rai coast to Saidor.

However, with the advance now taking them ahead of their supply system and the arrival of more Australian troops increasing the logistic problem, the Papuans began to run short on food and were placed on reduced rations for a number of days until an airdrop could be organised.

[204] In the latter half of 1943 the Australian government decided, with MacArthur's agreement, that the size of the military would be decreased to release manpower for war-related industries required to supply growing British and US forces in the Pacific.

[211] Yet the Australian military had held strong misgivings about the establishment of the PIR, and it had only been undertaken out of necessity, with the effectiveness, discipline and reliability of native troops questioned in some quarters, while training them in the use of weapons was seen as potentially creating a problem for the post-war administration.

In the north, it was planned that the Japanese would be forced into the narrow Bonis Peninsula and contained there while, in the centre, the seizure of Pearl Ridge would give the Australians control of the east–west avenues of approach, as well as affording them protection against further counter-attacks and opening the way for a drive to the east coast.

[255][Note 11] Although the number of Papuans that served in the conflict was relatively small in comparison to the Australians or Americans, being used in scouting and patrolling and often attached to far larger formations or in support of Allied intelligence, Sinclair argues that they had filled an important role out of proportion to their size.

[261] Despite initial disapproval from some prominent settlers prior to the war, the Papuan and New Guinean soldiers also came to be thought of highly by many senior Australian officers who considered them "...fighters skilled in stealth and surprise attack, men whose knowledge of the bush and experience in tribal warfare could advance the Allied cause.

[265] Yet the experience of the war forever altered PNG, helping to change the perceptions of many Papua New Guineans of relations between the races from that which had existed in pre-war colonial society, with many coming to view themselves as the equals of Europeans as a result.

[266] In the years immediately following the war the Australian Army considered re-establishing a military presence in Papua New Guinea, although there was some opposition among the colonial administration and white settlers to the raising of native units, echoing previous concerns.