Also known as exudative cloacitis, the debilitating disease causes inflammation of the lower digestive and reproductive tracts.
The disease causes the birds extreme pain and, in severe cases, if left untreated, it can stop reproduction and cause death.
Lead author and University of Otago microbiology and immunology postdoctoral fellow Dr Rebecca French said crusty bum had been present in the kākāpō population for about two decades.
She said the number of cases had been increasing across their widespread habitats over the past four years.
"This is definitely another challenge for kākāpō conservation," she said.
"Eventually, the lesions become crusty."
She said the cause had been a mystery, until now.
Researchers have used cutting-edge genomic tools to find the culprits — three bacterial species working together cause the condition.
The bacteria likely come from external sources, such as soil or water, or cross-species transmission, highlighting the need to investigate the environment on the islands where kākāpō live.
"Our main aim at the moment is to try to take this disease off their list of challenges," Dr French said.
Senior author and fellow Otago microbiology and immunology researcher Prof Jemma Geoghegan hoped the research would lead to more effective treatments.
Prof Geoghegan said such prevention strategies included habitat modification and biosecurity measures and potentially the development of a vaccine or immune-boosting medicine tailored to the bird’s unique physiology.
"Healthier kākāpō mean better survival and breeding success — a crucial step toward the long-term recovery of this taonga species."
Dr French said she was pleased to have been involved in the work.
"I’ve been passionate about kākāpō for many years, including spending time volunteering on the island of Whenua Hou, for the Kākāpō Recovery Team and it’s incredibly meaningful to be able to contribute to their conservation ..."
