A court battle over damage to a sacred site in the Kakadu National Park will head to the Northern Territory Supreme Court.

Parks Australia, which jointly manages the land alongside the Gunlom Traditional Owners is accused of breeching conditions obtained to build a walking track.

The Aboriginal Areas Protections Agency says the track was built without proper authority with chairman Bobby Nunggumajbarr saying proceedings would go ahead despite losing senior Gunlom custodian and Jaowyn traditional owner Mr Markan.