Buildings at south Auckland's Middlemore Hospital face costly upgrades as some of the walls are filled with rot and mould, but hospital bosses say patients are not at risk and remedial work is on the way.

According to Counties Manukau District Health Board, four of more than a dozen buildings - the Scott Building, Kidz First building, McIndoe Building and Manukau's Super Clinic complex - are suffering "weather tightness issues".

"In a few locations in 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 DHB says in response to papers released, initially to RNZ, under the Official Information Act.

Construction firm Hawkins designed and built all four buildings and the DHB reached a legal settlement last year. Terms are confidential.

DHB acting chief executive Gloria Johnson says they have been aware "for some time", at least since 2012 in two of the buildings, that there were leaking problems. Fixing them is still an ongoing, and expensive, issue.

A report by surveyors Alexander & Co in 2017 found there had been a "systemic failure" of the cladding, leading to water damage and timber moisture. It recommended it be fixed within five years.

The report referred to significant fungal and bacterial growth, brown rot and Stachybotrys - exposure to the latter can cause severe illness.

Ninety per cent of the timber framing is decaying in the Kidz First building, with moisture levels at 98 per cent.

"The time frames for repair are critical as the moisture damage of these buildings is in places close to breaching the internal linings," the report said.

Middlemore handles 91,000 patients and 350,000 outpatients a year, with almost 5000 staff.

A Counties Manukau DHB spokeswoman told NZ Newswire they would not comment as they were in the middle of commercial negotiations but said the problem would be fixed and there was no immediate risk to patients.