There was no harbour at Aitape, just an open roadstead and thirteen miles of beach. The beach grade was such that a Liberty ship wharf would have been over 200 m long. Instead, a short jetty was provided for shallow draught lighters in fair weather. The amphibian engineers of the US 533rd EBSR had some 150 landing craft but only 6 US Navy LCTs, 41 LCMs and 20 DUKWs were actually used in October. Calm seas prevailed from May through September but then the northwest season caused heavy swells, reducing the rate of discharge of ships to around 40% of the normal rate and an October storm destroyed the fuel jetty, requiring POL to be landed in drums.
The discharge of Australian cargo proceeded smoothly until late November 1944 but the port's resources became stretched as the Americans began shipping out. The GHQ Regulating Officer at Aitape gave priority to departing units in view of the deteriorating situation on Leyte and the discharge of Australian stores did not keep pace with consumption and reserves began to decline and by 28 December there were only ten days’ rations in the supply depot, although sufficient reserves were on board five vessels awaiting discharge that held the 30,000 tons of cargo 270 vehicles and 2,000 personnel. GHQ expressed concern but directed that the priority continue to be given to loading the outbound ships. From GHQ's point of view, Aitape was but a small part of a shipping crisis that involved 221 ships in December 1944 and resulted in the US Joint Chiefs arbitrarily cancelling sailings and ordering the return of ships.
Logistical units worked around the problem. In early January 1945, First Army gave permission for surplus stocks of American rations to be transferred to the Australians. Still, by February, rations were down to seven days, as was avgas, which had to be reserved for supply dropping aircraft, grounding RAAF close air support aircraft. The 126th General Transport Company helped unload ships while awaiting the discharge of its vehicles. Transport was supplied in the meantime by the Americans. Some 500,000 rounds of belted .303 ammunition were dispatched from Lae to Aitape in small ships. Certain canteen stores were also in short supply, particularly beer and cigarettes. Stocks of jungle green shirts and trousers were low but only partly due to the shipping hold up, for there was always heavy demand for large sizes. First Army sent 14,000 pairs of trousers and 27,000 shirts on three ships that arrived in April and May. Another 10,000 shirts and 19,000 pairs of trousers were received at Wewak by 1 July. The 104th Advance Depot of Medical Stores arrived with an inadequate scale of medical stores. More were on the River Derwent, which arrived on 20 December 1944 but did not complete discharging until 25 January 1945. Until then, medical supplies were flown in from Lae.
On 5 February, General MacArthur ordered the GHQ Regulating Officer to give priority to S. G. Reid, which had arrived on 18 December 1944 carrying rations, and San Simeon, which had arrived on 28 December, carrying general cargo and he arranged for 12,000 drums of avgas to be loaded at nearby Hollandia. As a result, S. G. Reid was fully discharged on 15 February and San Simeon on 10 March 1945. Unfortunately, San Simeon carried Christmas parcels in the bottom hold, many of which were ruined by the prolonged period in the tropics. For the Army’s handling of the takeover from the Americans at Aitape, General Blamey was carpeted by the Army Minister, Hon. F. M. Forde. This was the most severe criticism of the Army’s logistics since the Papuan Campaign.