A period of reorganisation and training followed as the battalion was prepared for the rigours of jungle warfare. The battalion concentrated at the Nagambie Road Camp in central Victoria initially, but in late September moved to Greta in New South Wales. In October, after a period of intense training, the 2/6th was moved to Brisbane from where, on 13 October 1942, they embarked on the Dutch merchant ship "Bontekoe", bound for Milne Bay for the first of their two campaigns there against the Japanese. After arriving at Milne Bay, where the 17th Brigade was held in reserve, on 19 October they remained there until January 1943, when the battalion embarked upon the MV "Pulganbar" and several smaller coastal vessels and moved to Port Moresby. From Moresby, they were airlifted to Wau on 14 January. During the battalion's time around Milne Bay, they had suffered heavily from malaria and over 300 men were in hospital at the time the battalion deployed to Wau; consequently, it was severely understrength by the time it went into battle. Nevertheless, throughout late January 1943, the battalion was heavily involved in the Battle of Wau, then afterwards took part in the advance on Salamaua, during which it fought several key actions, including the fighting around Lababia Ridge in late June, before supporting the landing at Nassau Bay and the Battle of Mubo in July and then taking part in the fighting around Mount Tambu and Komiatum Ridge in August. During the fighting the battalion sustained casualties of 59 dead and 133 wounded.