After their return to Australia, a long period of reorganisation followed, during which the battalion was converted to the jungle warfare establishment, which saw its authorised strength fall from around 900 men to just over 800. Late in the war, in December 1944, they were then sent back to New Guinea to help round up an estimated 35,000 Japanese in the Aitape–Wewak region. The campaign lasted until the war ended and saw the 2/1st join the coastal advance towards the main Japanese base at Wewak along with the rest of the 16th Brigade.