But expert advice was that as long as the wall spaces were not open to ventilation into the hospital or near an air intake, patient safety would not be compromised by the fungal growth, she said.
Director of population health and strategy Margie Apa agreed, saying, "The safety of patients, staff and visitors is paramount and we have been assured by our infection specialists that the presence of fungal growth presents no safety risk.
"This is because a physical barrier will exist between the remediation work and patient areas and the work area is not open to ventilation or near an air intake, as has been correctly reported."
Work on all the buildings started around 2000 when the building code allowed for construction methods that have now been found to leak.
In the middle of last year the health board commissioned an independent expert appraisal of the buildings, which recommended immediate safety measures and remediation work within five years.
"The timeframes for repair are critical as the moisture damage of these buildings is in places close to breaching the internal linings," the report 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."
The report noted that of particular concern was the McIndoe ambulance bay because of the chance a cladding panel could fall from the building.
Kidz First and the Superclinic showed significant active fungal and bacterial growth and multiple references to brown rot and stachybotrys. In some parts the inner face of the plasterboard lining had been affected meaning the damage would eventually transfer to the interior of the building.
The moisture content reading in the framing hit 95 per cent in Kidz First and 80 per cent in the Superclinic. Decay was found in 90 per cent of the locations tested at Kidz First.
Some remedial work had already been done but it was not comprehensive.
Investigations revealed the cladding on the Scott Building needed to be replaced because the original cladding failed, resulting in water getting into the building and causing damage.
The McIndoe building had less fungal and bacterial growth, but future decay was possible. The report referred to cladosporium, dematiaceous fungus and stachybotrys spores. Extensive remedial work had been done.
New Zealand Nursing Organisation industrial adviser Lesley Harry said the organisation's members were significantly concerned, and representatives had already requested an urgent meeting with the health board about the issue.
"The report paints a very grim picture indeed and we are concerned about the patients and staff that are in the facilities," she said.
She said members would be seeking assurances from the health board that it was prioritising the health of staff and patients.
She said it was not good enough that staff had to hear about such a major issue through the media and expected the district health board would have informed those affected as soon as the magnitude of the problem was realised.
Johnson said Counties Manukau Health issued proceedings against Hawkins Construction North Island Ltd, which built the buildings, in 2012 but early last year a confidential settlement was reached.
Health Minister David Clark said an extra $11.5 million in funding for building works at Middlemore had been signed off earlier this week, taking the total cost of the project to $27.5m.
The money would be used for re-cladding the Scott Building.
"The DHB identified the Scott Building as its top priority," Clark said.
"The DHB has been managing this situation for some years and a range of investigations, remediation and safety measures have been adopted. But more work is obviously required and I will be seeking answers directly from the DHB about its plan to deal with this situation."
Clark said it was important to note patient safety was not at risk as long as the rot and mould were contained within the walls.
"That will be of little comfort to the people of Counties Manukau who rightly expect that their hospitals are up to scratch," he said.
"This Government will not sit back while patients are treated in decaying facilities."
