Australia has recently experienced the largest poultry outbreak of highly pathogenic avian influenza (HPAI) in the country’s history. In an unprecedented series of events in May and June of 2024, poultry outbreaks were detected in two states and one territory, each involving independent spill-over events from wild birds. The CSIRO Australian Centre for Disease Preparedness (ACDP) collaborated with state partners for virus confirmation and sequencing during the outbreaks. We used novel workflows to rapidly obtain whole HPAI genomes and determine epidemiological linkages between outbreaks, providing critical data for on-farm management decisions. Complete genomic analyses were frequently reported within 8-10 hours, which was only possible through the development of the Oxford Nanopore MinION as a rapid high-throughput sequencing platform. The first detection in May 2024 was in the Meredith area of Victoria, where the virus was quickly sequenced as H7N3 HPAI. Two days later, samples were received from a tracing property near Terang, which were expected to be the same virus; however, genomic sequencing revealed this to be a H7N9 influenza and an independent spill-over event. The H7N3 virus was later detected on a further six properties in the Meredith / Lethbridge area, while the H7N9 virus was not detected again. About a month later, a poultry submission from the Greater Sydney Basin in NSW raised concerns of H7N3 spread from Victoria. However, sequencing later the same day identified it as a H7N8 virus, indicating a further independent spill-over event. This H7N8 virus was later detected on another property in NSW and a tracing property in Canberra. The detection in poultry of three independent H7 HPAI spill-over events within months is unprecedented in Australia. The use of rapid whole genome sequencing significantly enhanced ACDP’s response to the HPAI outbreaks, revealing critical epidemiological links and more actionable insights for management decisions.