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Road and rail lines remain closed and communities isolated across inland South Australia after widespread flooding, with the region bracing for more heavy rain.

A severe weather warning remained in place across the state's north on Tuesday with falls of up to 150 millimetres expected.

Food and other supplies have been airlifted into Coober Pedy with locals warned the Stuart Highway, the main access to the south, will remain closed for up to 12 days.

Pumping is being explored as an option to allow repair crews access as soon as possible.

Alternative routes are also being considered, with defence officials examining the possibility of using roads within the Woomera prohibited area.

A similar time frame has been placed on the restoration of rail lines linking SA to both the Northern Territory and Western Australia, with the Australian Rail Track Corporation working on 18 separate damage sites across 300 kilometres.

On Monday night, heavy rain lashed the state's Indigenous APY lands with Ernabella recording more than 100mm.

The deluge extended as far south as Port Augusta which had more than 50mm in a three-hour period, enough to turn roads into rivers and leave the town's main oval underwater.

State Emergency Service Chief Officer Chris Beattie said it was too early to determine the full extent of the damage across the state as he again urged people to cancel any planned travel to the north.

A working group has been established to bring together data on damage from local councils and state agencies.

Mr Beattie said most outback communities were well stocked with tinned and frozen foods while some were running short of fresh vegetables and meat.

"At this stage, we're quite comfortable with the food supplies for most of those communities," he said.

"Having said that, as this event protracts and the roads remain closed for longer periods, we will be looking at the need to resupply some areas."

The Bureau of Meteorology said the tropical system responsible for SA's soaking would steadily move to the east on Wednesday, leaving fine and dry conditions across most of the state.

© AAP 2022

Photo: A supplied image obtained on Monday, January 31, 2022, of Air Force Aviators loading supplies onto a C-27J Spartan aircraft at RAAF Base Edinburgh, north of Adelaide, bound for Coober Pedy, South Australia. Food relief is on its way to South Australia's north after heavy rain cut freight access to Coober Pedy and surrounding regions. (AAP Image/Supplied by Department Of Defence, LAC Stewart Gould)

Relief food supplies have been flown to Coober Pedy, in South Australia's north, after heavy rains cut road and rail links to the region with locals still facing a "perilous" situation.

Four RAAF flights were scheduled out of Adelaide on Monday with two more on Tuesday carrying 20 tonnes of groceries and other essentials.

More could be sent depending on the prevailing conditions and the needs of locals.

Brigadier Graham Goodwin said the force was ready to help out in any way it could.

"Our principal duty here is to assist the local community of Coober Pedy and the outlying areas, giving them surety and certainty of their food supplies," he said.

"The people are not going to be left without what they require. We are there to help people at a time of crisis.

"Let me assure the people of Coober Pedy, there will be food coming, there will be supplies coming."

With train tracks washed away and roads underwater, including the Stuart Highway, the inland drenching has also disrupted food and other supplies to both the Northern Territory and Western Australia.

More rains are forecast across SA's north this week, with up to 200 millimetres possible in some parts.

On Monday, the Bureau of Meteorology issued a severe weather warning for the region, saying dangerous and life-threatening flash flooding was possible.

State Emergency Service Deputy Chief Officer Liz Connell said locals should be prepared for more severe conditions and should keep clear of floodwaters.

She also urged motorists to delay any travel plans to the area with many roads still closed.

"We are expecting more rain over the next 72 hours and are expecting that will create more challenges in getting vehicles through and getting supplies to that community," she said.

Premier Steven Marshall said more rain would put extreme pressure on an already "tenuous" situation as he also called on people to cancel any unnecessary travel to the state's north.

"It is a perilous situation at the moment. This additional rain is creating havoc," he said.

"I think we've still got a couple of worrying days ahead of us.

"There is a double-edged sword because for some communities this is very welcome rain. But it is causing major problems with infrastructure and it's cutting off communities. This is of great concern."

Current estimates suggest regular rail freight routes will remain closed for at least another 12 days and possibly longer.

The Australian Rail Track Corporation said repairs were underway along a section of track more than 300 kilometres long while a small section remained inaccessible.

"Additional contractors are now on-site to assist ARTC crews and works include building access roads, ensuring supplies can get to damaged locations and supporting restoration works," a spokesperson said.

"We want to reassure our customers and the community that we will restore these links as quickly as possible."

Damage reports for roads across SA north continued to be hampered by high water levels making full assessments impossible at this stage.

A 14-day major emergency was declared in South Australia on Friday, allowing the state's Police Commissioner Grant Stevens to direct the movement of freight, ensure food security and co-ordinate relief efforts.

© AAP 2022

Photo: A supplied image obtained on Monday, January 31, 2022, of Air Force Aviators loading supplies onto a C-27J Spartan aircraft at RAAF Base Edinburgh, north of Adelaide, bound for Coober Pedy, South Australia. Food relief is on its way to South Australia's north after heavy rain cut freight access to Coober Pedy and surrounding regions. (AAP Image/Supplied by Department Of Defence, LAC Stewart Gould)