A property developer has won a noise complaint case against the country's largest military airbase, prompting the Defence Minister to declare that urban sprawl may now be a "threat to our national security".

The Environment Court today released a decision ruling in favour of developer Neil Construction Ltd by issuing a declaration that Whenuapai airbase must comply with noise restrictions when it does late-night testing of aircraft engines.

The court, however, stopped short of halting the work – saying the Defence Force had 20 days to lodge an appeal before the ruling came into force and could keep working while it was considered.

Much of the complex case hung on whether testing of engines could be considered "aircraft operations" under special noise guidelines that apply to the base, with the court ultimately ruling that it could.

"If one were to ask the neighbours how they were aware of aircraft operations, they would likely say that it was when they could hear aircraft engines operating," the court said in part of its decision.

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In a statement, Defence Minister Ron Mark said there was no question the ruling could impact the military's use of Whenuapai - which was established before World War II.

"I understand this could mean moving the testing to another area of the base," he said.

"To me, that makes the noise somebody else's problem and would impose significant cost on the taxpayer - I understand this would be in the millions of dollars".

Mark said the precedent set by the decision could have serious impacts on the Defence Force's operations nationwide.

"It could put in jeopardy our ability to conduct search and rescue, and disaster relief operations outside of commercial office hours," he said.

"Looking at the ruling it makes me wonder if perhaps one of the threats to our national security is property development."

Mark said the NZDF's legal team would report back next week with advice about further steps.

Comment has been sought from Neil Construction.

Mark earlier this year announced the future of the RNZAF Base Auckland at Whenuapai was under review – along with the rest of the Defence Force estate - saying it was increasingly under threat from growing urbanisation near its boundaries.

"A property developer who has bought land right next to the base, which has been there for decades, is complaining that we run our engines at night or after dark," Mark told the Herald in July.

"This reverse nimbyism is having a massive impact on the ability of the Defence Force to operate today."

The decision also comes after outgoing Air New Zealand chief Christopher Luxon said the company was in the final stages of testing the viability of flying commercially from Whenuapai.

The company declined to comment on the Environment Court ruling on Friday.