The federal government has confirmed it will fight a Northern Territory agency that claims it illegally disturbed an Aboriginal sacred site at a former movie set in Kakadu National Park.

The NT’s Aboriginal Areas Protection Authority has filed a criminal charge against Parks Australia for carrying out uncertified work at Gunlom – a cascading waterfall that appeared in the movie Crocodile Dundee.

The director of national parks on Friday formally entered a plea of not guilty in the NT Local Court.

The plea allows the Local Court to refer the matter to the Supreme Court as a special case.

The Commonwealth Attorney-General is listed as an interested party in the case, which is set to become a constitutional battle.

Parks Australia is accused of building a walking track to the top pools at Gunlom without permission from the Indigenous custodians.

AAPA alleges the track was constructed close to a restricted ceremonial feature against the wishes of the World Heritage-listed park’s traditional owners and without an authority certificate, which is issued after consultation.

Before AAPA issues an authority certificate, it consults traditional owners about the sites to understand how they should be protected, and what restrictions and conditions should be applied to the proposed works.

Parks has agreed to remove the offending section of track and a certificate has since been sought and obtained.

It had urged the AAPA to drop the criminal charge but that was refused.

Acting director of national parks Jody Swirepik has previously said the body is committed to rebuilding the relationship with traditional owners.

The maximum penalty under NT law for carrying out work on a sacred site without a certificate is $314,000.

The Supreme Court is expected to schedule a hearing for the special case early next year.

Parks Australia, part of the federal government’s environment department, has been contacted for comment.

-AAP