Sydney's Royal Prince Alfred Hospital confirmed six patients in its transplant unit were caught up in the fungal cluster in late 2025.
The cause of the infection was Aspergillus, a common mould found in things like soil, dust and damp environments.
People are unlikely to become unwell from Aspergillus but it can be particularly damaging for certain individuals with weakened immune systems, a Sydney Local Health District spokesman said.
"Fungal infections are a known risk for patients who are significantly immunocompromised, including patients undergoing organ transplant procedures," the spokesman said.
"(The district) extends its deepest condolences to the families of the patients who died at Royal Prince Alfred Hospital and acknowledges the impact on all patients and families."
The outbreak occurred between October and December 2025.
The hospital is the middle of a $940 million redevelopment.
Health authorities indicated the construction works were the cause of the fungal infections.
Infectious disease clinicians investigated the outbreak and safety measures were ramped up, including a deep clean of the ward, upgrades to air-filtration systems and comprehensive air testing.
Patients were moved out of the transplant ward while the remedial efforts were performed.
At-risk patients were given antifungal medication after consultation with clinicians.
NSW Chief Health Officer Kerry Chant convened an expert panel to advise on risk mitigation and it declared the ward safe to reopen on February 9.
"RPA is a leader in transplant surgery, with nearly 60 years of experience performing kidney transplants and 40 years in liver transplants," the district spokesman said.
"We reassure patients and the community that RPA Hospital continues to be a safe place for care and we have put in place robust policies and procedures to help prevent any further fungal infections."
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