The storm, which weakened to below cyclone strength after crossing the coast at Cape Shield in remote eastern Arnhem Land on Sunday, is still expected to cause widespread damage as more rain falls on already sodden ground and swollen rivers.
The ex-cyclone is forecast to continue its path into Western Australia on Monday, bringing heavy rain and strong winds.
The tropical low tracked past Katherine overnight, impacting a major Northern Territory town already struck by widespread flooding from a previous storm.
The system will move over the Joseph Bonaparte Gulf on Monday, potentially strengthening again to a category-two cyclone, impacting properties in WA's Kimberley region.
Northern Territory Chief Minister Lia Finocchiaro said the weather system would lead to rising water levels across the region, particularly in Katherine, where the clean-up from floods a fortnight earlier was winding down.
"The ground is saturated, our rivers already full and any additional rainfall is going to make a significant impact," she said.
Katherine Mayor Joanne Holden said there was a sense of calm in the exhausted community as locals prepared for the latest weather event.
"They know what they need to do and they're just quietly getting around and doing what needs to be done, and the community is pulling together and helping each other out," she told AAP.
Major flooding was expected in Katherine from Monday afternoon.
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