It could take two weeks to repair flooded rail links from South Australia to Darwin and Perth.
Incredible pictures have been sent back from work crews which show the extent of the flooding damage for the first time.
Bridges will need repair as well as extensive lengths of line fixed.
The Stuart Highway remains cut and one major supermarket is taking the extraordinary step of sending grocery supplies from Adelaide via Mount Isa in Queensland to reach the NT.
Work crews have arrived at some of the rail washouts east of remote Tarcoola in outback SA to find at least eight locations where damage has been caused.
"The damage is significant in nature and heavy machinery and materials will be required to fix the rail line," a spokesman for Australian Rail Track Corporation said.
ARTC say the weekend's rain, which dumped up to 200mm in quick time in the usually dry desert country, caused flash flooding as can be evidenced in the pictures.
Experts now say the rain was a 1 in 100/200 year event.
ARTC crews worked through the weekend to inspect and asses track with some locations identified as being damaged.
Crews worked quickly to repair the damaged lines, however access limitations via rail and road prevented some areas from being inspected.
More rain on Monday further hampered repair work with storms forecast for tomorrow.
"Our crews worked tirelessly to repair the damaged rail infrastructure where possible and where conditions allowed," the spokesman said.
"Whilst crews worked to fix issues caused by rain late last week, the rainfall on late Sunday/Monday caused additional damage."
Work crews are having trouble accessing some of the worst trouble spots because many are still under water.
"Major earthworks are required at several locations to restore the track," the spokesman said.
"Additionally, access to these locations is challenging as major highways were closed due to washaways. Other local roads are cut due to flooding.
"Up to eight sites are inaccessible at this stage due to flood waters."
The rail authority sent a helicopter out on Tuesday to further inspect the damage and help develop a recovery plan.
ARTC is working with South Australian authorities and the State Emergency Services on exploring options for support from mines and local contractors in the area to aid with recovery.
ARTC expects repairs of the damaged rail infrastructure to take at least 12 days.
"We want to reassure our customers and the community that we will restore these links as quickly as possible.
"ARTC will provide regular updates on operations as information becomes available."