Toxic firefighting foam has contaminated several Defence Force bases around the country, including Ngataringa Bay, adjacent to the Devonport naval base.
Radio NZ has reported that Defence Force chief Tim Keating warned new Defence Minister Ron Mark of the contamination in a November briefing paper, obtained under the Official Information Act.
The report described the pollution at Devonport and the Whenuapai airbase as a "significant land contamination issue".
It also stated that a well, which previously provided drink water for Blenheim's Woodbourne airbase, was contaminated beyond safe levels and the Defence Force is still trying to determine how long it has been undrinkable.
Defence Force publicly revealed contamination at Woodbourne and Palmerston North's Ōhakea airbase in December, but this briefing paper suggests it also knew a wider threat existed across most defence facilities.
"Soils, sediments and site runoff at the Sea Safety Training Squadron on the shoreline of Ngataringa Bay are contaminated with PFAS compounds," said the report.
Radio NZ has previously reported an ongoing testing programme at Devonport.
"This step will inevitably result in media attention and public awareness of PFAS as an environmental and potential health issue not only for the... Defence Force, but also for other users of firefighting foam nationwide," Lieutenant General Keating told Mr Mark.
PFAS is a long-lasting manmade chemical that has been linked to two types of cancer, and other health and environment risks around the world, although New Zealand health authorities claim research has been inconclusive.
Radio NZ reports the Defence Force stopped using this type of firefighting foam in 2002, but the chemicals take thousands of years to break down and contamination levels remain high.