The Defence Force says it has put in a special filter system at its Auckland naval base because toxic chemicals used two decades ago keep getting into the wastewater.
Devonport base installed the specialised filters last November to deal with PFAS chemicals from historic use of now-banned firefighting foam.
PFAS are a threat in parts per trillion, do not biodegrade and biomagnify up the food chain.
The PFAS fluorine foam used up till 2002 by Defence for firefighter training has polluted Ngataringa Bay, an endangered bird habitat, next to the Sea Safety Training Squadron. Levels in fish in the Waitemata Harbour were low.
"PFAS continues to leach from the surfaces of steel, concrete and asphalt," Defence said.
"Residues have also been detected in the soil.
"High tides and heavy rain bring PFAS from groundwater into the site stormwater system and thence to the on-site water treatment system."
It is not using PFAS foams anymore, it said.
Training with them is banned, though that ban was recently breached at the oil refinery in Northland.
Investigations at Devonport in 2019 showed the Defence Force it had to do something about PFAS discharges that were non-compliant.
Problems with the old treatment system "exacerbate the accumulation of PFAS", a report in late 2020 said.
"NZDF committed significant resources to temporary storage of the intermittent discharge water and subsequent transfer to ChemWaste for treatment and disposal" from 2019 until starting up the new filter.
Defence says the new Granulated Activated Carbon filter has fixed the discharges.
PFAS sticks to bits of carbon as water flows through the system.
As for the contamination at its other bases, revealed by a land revaluation report released to RNZ, Defence says it is complying with health and safety, and environmental, legislation and regulation.
The report gave a rough estimate of $28 million to partially remediate 21 sites.
Devonport scored almost 400 for actual or potential contamination, well ahead of any other base and up against several other sites at zero.
The report said NZDF should improve how it assesses contamination risks.
But Defence said its investigation and reporting methods "are fit for purpose".
These use an official Hazardous Activities and Industries List (HAIL) to rank sites for further investigation based on risk.
"Where the ranking ... indicates a need for remediation, then that work will be undertaken," Defence said in a statement on Friday.
If it showed a risk of contaminants leaking off a base, that would be looked into, too.
The contamination was mostly decades old, and current practices and managements were at a "different, higher standard".
Defence's priority for clean-ups under a $2 billion 15-year estate upgrade, are to deal with toxic lead found at some of its many houses. It's also trying to deal better with lead contamination at its firing ranges.