Forecasters had warned that a tropical low brewing north of Darwin over Christmas could intensify into a category one Boxing Day cyclone.
But the Bureau of Meteorology downgraded the alert late on Saturday, saying the weather system would remain a tropical low.
It crossed the coast about about 150 kilometres southwest of Darwin overnight and is currently moving slowly southeast across the Daly region.
The bureau said parts of the Top End have been hit by heavy rain and squalls.
A severe weather warning has been issued for people in Daly, Tiwi, Arnhem, and Carpentaria regions.
Heavy rainfall that could lead to flash flooding is expected to continue throughout Sunday across the Arnhem, Daly, Tiwi and northwest Carpentaria districts.
Rainfall of 150 to 250mm and isolated falls to 300mm are possible.
Damaging winds with gusts of up to 100 km/h with monsoonal squalls may develop in coastal areas.
The extreme weather conditions may push further east and south into the Carpentaria and Arnhem District later in the day
A flood watch is also current for parts of the Top End.
