The weather bureau has cancelled its cyclone warning for parts of the western Top End in the Northern Territory and Western Australia but warns of the prospect of more torrential rain.
A tropical low on the coast, west of Darwin, is no longer expected to develop into a cyclone.
Bureau regional director Andrew Tupper says the system is causing heavy rain to fall along the western Top End.
He says it could cause flooding in low lying areas in the Darwin and Kimberley regions.
"Just because the cyclone warning is finished does not mean there is nothing happening," he said.
"Last time we had a cyclone go inland we had the Stuart Highway and the trainline cut off."
The monsoonal system brought wild weather to Darwin overnight and this morning.
Up to 200 millimetres of rain has fallen in some parts of the Top End.
The deluges forced the closure of dozens of roads in the city and Rural Area.
Forecaster Graham King says monsoonal conditions will continue as the low moves closer to the coast.
"There is the possibility of some very heavy rainfall extending through the western Top End into the Victoria River region and maybe even further down into the Roper Mcarthur in coming days," he said.
"I think anywhere north of that monsoon trough has got the chance of some heavy falls."
The Territory Education Department says all but four of the schools that were closed today due to the cyclone warning will be open tomorrow.
Schools at Bulla Camp, Nganambala, Nganmarriyanga and Peppimenarti will remain closed for another day.
Meanwhile, the East Kimberley emergency services say the areas of Wyndham and Kununurra could still experience flooding and heavy rainfall, despite the cyclone warning being cancelled.
SES District Manager for East Kimberley Graham Sears says after a teleconference with the Territory weather bureau the West Australian "Blue Alert" has been downgraded to a weather watch.
He says bureau indications show the tropical low could still bring significant rainfall to Wyndham and Kununurra.
"The indicators are we will probably get anywhere between 100 millimetres and 200 millimetres of rain," he said.
© ABC 2012
13:34 EDT Very hot, dry and windy conditions have caused the issue of a Catastrophic Fire Danger for the Eucla in Western Australia.