The Department of Defence says it will not accept any liability for aircraft noise if planning authorities approve a new town north of Raymond Terrace.
Hunter and Central Coast Regional Planning Panel deferred a decision on the Kings Hill development in December to commission its own study into the area's koala population.
Defence opposed the residential rezoning of the land 10 years ago and reiterated that stance this week.
"Defence assessed that future residents would very likely be impacted by the introduction of the F-35A Joint Strike Fighter into RAAF Base Williamtown," a spokesperson said.
"Defence ... is committed to undertake flying operations in a manner considerate of local communities while maintaining the safe operation of aircraft and meeting operational and training requirements.
"Defence will not accept any liability based on aircraft noise."
The Defence website's Australian Noise Exposure Forecast map for Williamtown and the nearby Salt Ash bombing range does not highlight noise effects directly above the Kings Hill site, which is next to the Pacific Highway six kilometres north of Raymond Terrace.
But the 2025 forecast includes the disclaimer that "actual noise levels can vary depending on actual aircraft movements and environmental conditions".
A spokesperson for Kings Hill Development said the land was not under official flight paths, and a Port Stephens Council spokesperson supported that view.
Defence assessed that future residents would very likely be impacted by the introduction of the F-35A Joint Strike Fighter.
Department of Defence spokesperson
The council recommended approving concept plans for the 3500-lot housing estate spread across 270 hectares of bush along the highway and Six Mile Road.
But concerns from local groups such as Port Stephens Koalas, the Greens and EcoNetwork over the potential loss of koala habitat and other endangered species forced an adjournment.
Port Stephens Greens secretary Caitlin Spiller said community groups were pleased the panel had heeded their concerns and called for independent advice.
Representatives for Kings Hill Development said investigations by experts over 18 years had ensured a conservation plan that protected important habitat.
A Kings Hill spokesperson said the panel's decision would "provide the community with confidence in the outcomes".
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