Briefing documents seen by AAP show health authorities failed to move transplant patients from a ward adjoining major construction sites despite knowing the danger to the immunocompromised.
Scrutiny of the lead-up to the two deaths comes as a snap review into hospital infrastructure shows outbreaks of cockroaches, possums, birds and insects at health facilities across NSW.
The briefing from health officials related to the fungal outbreak was authored in January, two months after the two patients died at Sydney's Royal Prince Alfred Hospital.
The cause of the infection was Aspergillus, a common mould found in soil, dust and damp environments.
Six patients in the transplant unit were affected by the fungal cluster from May to December 2025, health officials confirmed on Monday.
The transplant ward was abutted to the construction site at three different points, including a balcony accessible by patients, the briefing documents show.
"If possible, relocate at-risk patients who are adjacent or near to the construction zone," mandatory procedure documents from the local health district state.
But the procedure was not followed, despite the risks of invasive fungal infections (IFI) to vulnerable patients being well known.
"There are clear links between IFI and construction activity in the published literature," the secret briefing says.
While most people are unlikely to become unwell from Aspergillus, the briefing documents show authorities were aware of the high danger to the severely immunocompromised transplant patients on the ward.
A mortality rate between 60 and 80 per cent is estimated for patients contracting an invasive fungal infections, the document says.
Furthermore, knowledge of the outbreak was kept from the relevant minister for more than a month after health authorities discovered it.
NSW Health Minister Ryan Park's office was alerted on Christmas Eve to the possibility of deaths relating to a fungal outbreak at the hospital.
But Mr Park admitted on Monday he was unaware of the deaths and illnesses until well after his return from holidays on January 5.
He said the time he was told would have been around "the first part of February".
"I don't have a date where I've written something down," he told a budget estimates hearing.
The ward was reopened on February 9 on advice from an expert panel.
Opposition health spokeswoman Sarah Mitchell said the communication breakdown in the department was unacceptable.
"How can you not know when there's been a major outbreak and hundreds of people needed to be informed about it?" Mrs Mitchell asked Mr Park on Monday.
The troubles inside the 143-year-old tertiary hospital, often at the cutting edge of medicine, were followed on Monday by the revelation of substantial maintenance and pest issues across the state's 4400 health buildings.
There are 38 non-routine maintenance issues still unresolved from 2025, Mr Park said.
These include ongoing pigeon infestations at Tamworth and Royal Prince Alfred hospitals and five hospitals needing roof repairs.
"I would like every building to be perfect and new," Mr Park said.
"The challenge is that with a portfolio this size, you're always going to need to be on top of maintenance."
As well as maintenance problems, the snap probe identified major infestations in the past decade that were never reported.
Flies, cockroaches, birds and possums were found in major Sydney and Central Coast hospitals, including Westmead and Royal North Shore, between 2012 and 2019 without being reported in the press.
"If you're a patient, you deserve to be cared for in our hospitals, not having to avoid fatal mould, maggots (and) bird lice," Opposition Leader Kellie Sloane told reporters on Monday.
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