The unit carried out a total of 81 covert operations in the South West Pacific theatre, with parties inserted by parachute or submarine to provide intelligence and conduct guerrilla warfare. The best known of these missions were Operation Jaywick and Operation Rimau, both of which involved raids on Japanese shipping in Singapore Harbour; the latter of which resulted in the deaths of twenty-three commandos either in action or by execution after capture.
In his memoirs, former leading aircraftsman, Jack Wong Sue, claimed that Z Special Unit commandos in Borneo killed 1,700 Japanese for the loss of 112 commandos, as well as training more than 6,000 guerrillas. The activities of the commandos laid the groundwork for the Allied invasion of Borneo in 1945
Although the unit was disbanded after the war, many of the training techniques and operational procedures employed were later used during the formation of other Australian Army special forces units and they remain a model for guerrilla operations to this day.