The Stuart Highway, one of the most important trunk roads across Australia, is partially under water after days of cloudbursts.
The region near Glendambo in the state of South Australia, where the roads are completely submerged under the floods, is particularly affected, Australian media reported.
Broadcaster ABC on Friday showed drone footage showing the extent of the flooding in the outback.
Supply chains in the north of the country were interrupted, it said.
Trucks sometimes have to drive detours of up to 3,000 kilometers through the states of New South Wales and Queensland to reach the Northern Territory, according to the broadcaster "Sky News Australia".
Among other things, the remote outback town of Coober Pedy was completely cut off.
Citizens with health problems have been flown out by the Australian Air Force.
"Not only does the water have to recede, but we then have to assess the damage that the road has suffered before people can drive on it again," said local emergency services chief Trevor Arnold.
This is necessary because the Stuart Highway is mostly used by extremely heavy trucks.
The highway, which runs from south to north over a length of around 2700 kilometers, is considered one of Australia's dream roads.
It connects the towns of Port Augusta in South Australia with Alice Springs in the Red Center and Darwin in the Northern Territory.