In mid-1942, the battalion was withdrawn from the Middle East to help face the threat posed by the Japanese in the Pacific. A period of garrison duty was undertaken in Ceylon between March and July 1942, before they arrived back in Australia in August 1942. Following this, the 2/6th deployed to New Guinea in January 1943, fighting around Wau and then advancing towards Salamaua during the Salamaua–Lae campaign. They were withdrawn to the Atherton Tablelands for rest in September 1943 and subsequently did not see action again until later in the war, when they were committed to the Aitape–Wewak campaign in late 1944. The 2/6th remained in New Guinea until the end of the war, and was disbanded in February 1946, after returning to Puckapunyal the previous December.