New documents show Middlemore Hospital management has known for years the buildings are leaking, creating the toxic mould.
The rotten buildings include the children's hospital and the Manukau Superclinic and new documents show the decay is so bad it is in danger of breaching the walls and contaminating the air.
The Counties Manukau District Health Board faces a repair bill of tens of millions of dollars but says patient safety is not compromised so long as the fungal spores stay in the walls.
The documents also show the hospital's management have known for years the buildings were leaking but had not fixed them.
The information obtained under the Official Information Act includes an independent investigation report.
It has found significant fungus and bacteria inside the walls of four buildings - brown rot, fungus and Stachybotrys in multiple places.
Exposure to Stachybotrys can cause severe illness.
Ninety percent of the timber framing looked at in the Kidz First hospital is decaying, the wood soaked at up to 98 percent moisture levels.
"The timeframes for repair are critical as the moisture damage of these buildings is in places close to breaching the internal linings," the report to the district health board by surveyors Alexander and Co, said.
"Ad-hoc emergency repairs are unlikely to be an acceptable option as they present a risk to patients and staff and will adversely affect the smooth operation of the facility."
If any walls were breached, it would have to vacate those areas, the Counties Manukau DHB acting chief executive Gloria Johnson said in a report to RNZ accompanying the OIA response.
"At this time, clinical expert advice is that provided the wall spaces are not open to ventilation into the hospital, or near to an air intake, patient safety is not compromised by the fungal growth found," she wrote.
The other "real" risk at all four buildings is the cladding will fall off and hit someone as fixings into the rotten frames fail.
It's understood a two square metre piece of heavy cladding fell off the Scott Building in 2012, which first raised the alarm about the leaks.
Three major buildings at Middlemore Hospital at Otahuhu are compromised: the Kidz First hospital, and the Scott and McIndoe buildings; plus the big Superclinic 8km south in Manukau.
The Scott building includes medical, surgical and wards for elderly people; McIndoe has the National Burns Centre, and intensive care; Kidz First includes acute care for children with breathing difficulties and a neonatal unit.
Middlemore alone handles 91,000 patients and 350,000 outpatients a year, with almost 5000 staff.
"In a few locations to the Kidz First Building and the Super Clinic Complex, the inner face of the plasterboard linings had been affected by fungal growth and this damage will readily transfer to the interior of the building in the short to medium term," the investigation report said.
The DHB wants to do all the repairs while everything is kept running.
"The key issue is the need for this to be undertaken with the buildings fully operational as an acute hospital facility," Ms Johnson said.
Only the McIndoe building has had much remedial work done on it - but its ambulance bay is one of the worst spots of all, with a "high" risk that cladding would fall off.
All four buildings were constructed between 1999 and 2001, in the heydey of the leaky building crisis, before law changes in 2004 banned the use of untreated timber framing in walls.
The other factor to the four leaky buildings was "shortfalls in build methods", the DHB said.
The OIA reveals the DHB took an offshoot of Hawkins, Hawkins Construction North Island Ltd - now called H Construction North Island Limited - to court in 2012.
It reached a full and final settlement only a year ago. The board won't reveal the amount, saying this was confidential, even under the OIA.
The DHB has awarded that repair contract to Hawkins, the firm it sued over the Scott building.
The hospital first knew back in 2012 there was a problem at Kidz First and the Scott Building; it was a year or two later it found out about the others.