Manawatū's regional council says the Defence Force has to provide it with a plan on how it will avoid letting contaminants into waterways around Ōhakea.
Horizons Regional Council, in the Manawatū-Whanganui region, believes the Defence Force has been letting contaminants from aqueous firefighting foam into waterways and has issued an abatement notice to prevent it.
It has been carrying out a formal investigation into the discharge at Ōhakea air base.
Senior council manager Nic Peet said the probe had revealed enough information for it to warrant this action.
"I think you can take from the fact that we've issued an abatement notice that we certainly believe that it has happened and there'd be the potential for it to happen in the future."
The abatement notice means the Defence Force can no longer put water containing firefighting foam - which may contain toxins and chemicals - down stormwater drains.
That includes water used to wash foam off fire trucks, or onto land near the training area where it may enter waterways.
The Defence Force declined to be interviewed, but said it stopped using the firefighting foams at Ōhakea and at all of its bases in 2016.
Dr Peet said the abatement notice was a reflection that discharges had occurred and needed to stop.
The Defence Force is required to provide the council with a plan by 1 July that outlines what steps it has taken to avoid these discharges happening in the future.
Auckland Councillor Chris Darby is worried about a similar problem occurring in the Devonport Naval Base or Whenuapai Air Base and has asked the council to look into it.
The Defence Force has the right to appeal the notice.
Horizons Regional Council said it was in the middle of its formal investigation and there is potential it could take further action.
It has accused the Defence Force of blocking it from getting the information it needed to investigate the foam.
The use of the potentially toxic foams has been under investigation by an all-of-government team, which expanded the inquiry to include water and soil contamination last month.