The crossing at the East Alligator River, which is a major route to Oenpelli and Arnhem Land, has closed.
Northern Territory Infrastructure Department spokesman Sam Satsangi says the road shuts due to flooding every wet season.
Late rains this year have meant Cahills Crossing has stayed open longer than usual.
He says the crossing, about 230 kilometres east of Darwin, could be closed until April if the weather stays wet.
"The only other way that you can go to Oenpelli is the long way," he said.
"You have to go to the Central Arnhem Road, you have to take the road to Ramingining and come back from Maningrida back to Oenpelli, which is a fairly long route.
"But it's the only alternative route available."
© ABC 2013
16:06 EST The weather bureau has implemented a new system of forecasting the seasonal outlook called Predictive Ocean Atmosphere Model for Australia, or POAMA.