Defence Minister Ron Mark has used his powers to overrule a noise complaint ruling against the country's biggest military airbase on the grounds of "national security".

The Environment Court last month released a ruling in favour of developer Neil Construction Ltd, declaring Auckland's Whenuapai airbase had to comply with noise restrictions when it performs late-night testing of aircraft engines.

It prompted Mark to say urban sprawl was now perhaps a threat to the nation's safety and that there was no doubt the ruling could impact the military's use of the site.

On Tuesday, Mark announced he would be using special powers under the Resource Management Act to exempt Whenuapai from the noise rules.