The new deal extends the relationship with Alliance Airlines' business unit Alliance Aviation Services, which began in 2006, by a further 10 years until 2030.
Alliance will be the sole supplier for the service connecting Townsville, Cairns and Brisbane with the Cannington silver-lead-zinc mine in Queensland and the Groote Eyland Mining Company manganese operation in NT's Gulf of Carpentaria.
Alliance chief executive Lee Schofield said: "For the next 10 years Alliance will also be servicing South32's charter requirements from Darwin.
GEMCO is an opencut operation producing high-grade manganese ore that is shipped to South32's Tasmania manganese alloy plant and around the world.
The Cannington operation comprises an underground mine and processing plant, processing 3 million tonnes a year.