More rain has fallen and more is expected in the flooded areas in the north of the state where transport routes remain cut.

Repairs to the Stuart Highway and Trans-Australian Railway could be weeks off.

The RAAF involvement comes after the outback flooding was officially declared a Major Emergency over the weekend.

SA Police Commissioner and state coordinator Grant Stevens said, following advice from the Chief Officer of South Australian State Emergency Service Chris Beattie, it was determined a Declaration of a Major Emergency was appropriate.

"There has been significant damage caused to rail and road infrastructure over the last few days and this is threatening food security in some areas of SA, NT and WA,'' he said.

"A declaration of a Major Emergency will ensure a coordinated, state-approach to ensure food security and provide support if required by isolated communities.''

IN OTHER NEWS:

A RAAF C-27J Spartan, supporting the SA Government's declaration will depart RAAF Base Edinburgh to provide critical airlift of about 20 tonnes of essential food to Coober Pedy this morning.

Flash flooding in the outback from record rain a week ago has cut the Stuart Highway in several places in the north of the state, marooning travellers and cutting freight to the Northern Territory.

Rail lines are badly damaged near Tarcoola which has also stopped freight to Western Australia and the NT.

Some freight companies have chosen to use an incredible detour via Mount Isa in Queensland to re-stock the NT.

Tarcoola is so remote and uninhabited the Australian Rail Track Corporation was forced to send a helicopter out to survey the damage last week and the damage to lines has been shocking.

The ARTC issued an optimistic forecast of two weeks to repair most of the damage to washed out lines and bridges but water still covers some line.

The Bureau of Meteorology today forecast more rain for the area through to Wednesday.

The bureau said increased showers and thunderstorms are possible across the pastoral and Flinders districts.

A total of 63mm was recorded at Todmorden Station, several hours travel time to the north of Coober Pedy, on the weekend.

The heavy rain also fell in the area of the Stuart Highway.

"Rainfall totals until midnight Wednesday are expected to be generally 10 to 50mm over the pastoral and Flinders districts, increasing to 50 to 150mm over the central parts of the pastoral districts. Isolated higher falls of 150 to 250 mm with intense thunderstorms are also possible," the bureau has forecast.

"Increased water ponding and overland flow together with rises in local streams and creeks can be expected. Transport routes may be further impacted affecting community access and travel."