A second RAAF service began in Vietnam on 3 May 1966 when an advance party from No. 9 Squadron arrived at Vung Tau. The squadron's helicopters arrived on 6 June aboard HMAS Sydney and were flown to Vung Tau that day before moving to Nui Dat at the end of the month.
No. 9 Squadron's helicopters carried out a variety of roles in Vietnam. Most important were the transport of infantry and logistic support, but the helicopters were also used to drop leaflets over enemy territory. Some were also used in aerial spraying to rid the base of mosquitoes and, more aggressively, to kill vegetative growth around the base and to destroy agricultural plots in Viet Cong territory, denying the enemy a source of food.
Just two months after the squadron's arrival in Vietnam, two pilots were called on to drop ammunition to the beleaguered troops of D Company, 6th Battalion Royal Australian Regiment, at Long Tan. Flying in appalling weather at tree-top height; they dropped ammunition to the soldiers on the ground through driving rain and under intense Viet Cong fire. The squadron operated again that night, after the battle, to retrieve the wounded, guided only by the light emanating from the open hatches of armoured personnel carriers.
No. 9 Squadron was re-equipped with larger Iroquois helicopters in 1967. Now equipped with 16 helicopters, the squadron worked in conjunction with aircraft of the Royal Australian Navy Helicopter Flight Vietnam and United States forces, on the dangerous tasks of transporting men to and from patrols and evacuating wounded soldiers from the battlefield. On some occasions these operations ended with the death of helicopter crewmen and the destruction of the aircraft.
The last members of 9 Squadron left Vung Tau on 17 December 1971. Six squadron members were killed on operations, and another man, attached to the squadron from No. 1 Operational Support Unit, was also killed.