A toxic mould infested Middlemore Hospital building is to be re-clad, while patients are inside.

A Ministry of Health paper looking at fixes for the leaky 500-bed Scott Building says re-cladding is a high-risk operation.

It says buildings are generally empty when they're re-clad, so the procedure to fix the Scott Building with patients still inside, is believed to be unprecedented in New Zealand.

One of the biggest fears is that toxic mould spores will enter clinical areas where they'll be especially dangerous to patients with reduced immunity.

Counties Manukau District Health Board chairman Mark Gosche says they have no other choice.

"At times Middlemore Hospital runs at absolutely 100 per cent capacity, especially through the winter so this is an option that has to be carefully managed."

He said patient safety is their number one concern and so the process will take time.

"There does have to be a careful process where you build an internal wall to prevent any issues for those still inside the building - as a result, this is a long process which will take over two years."