But he said warnings remained for Mitchell Plateau to Dundee Beach, including Wadeye.
"Communities in the western Top End are still experiencing rain and wind gusts and we remind people to take care and drive to conditions," he said.
"Communities in the Daly River region, including Wadeye should be aware of river levels and road conditions and restrict all unnecessary travel."
Damaging winds gusting up to 95 km/h were recorded along the NT's Bathurst Island coasts, where a record 384mm of rain fell while winds blowing at up to 80 km/h ripped through Darwin overnight.
The category one system formed yesterday south of the Tiwi Islands and is heading southwest and was estimated to be 130km west of Darwin, moving at 12 km/h.
It is expected to intensify to a category two by the time it crosses the Kimberley coast later today.
The WA Department of Fire and Emergency Services is urging residents from the NT border to Kuri Bay in the Kimberley to prepare for dangerous weather including flooding caused by above-average tides and large waves.
- AAP