Rail movement between Perth and the eastern states will be shut down until Thursday at the earliest, with 10 sections of the line around 400 kilometres east of Kalgoorlie-Boulder underwater due to heavy rains.
An Australian Rail and Transport Corporation spokesperson said all rail movements across the Nullarbor had been halted since early Wednesday morning.
"There is major flooding all through the centre, there are certain branch sections that are open to allow trains some movement, but across the Nullarbor at the moment there's no movement," the spokesperson said.
The track was originally scheduled to be re-opened on Monday, but heavy rains overnight stretched that timetable out to Thursday.
"The whole operation has been slowed because there has been more rain overnight; it has slowed down everything and increased the deluge on the track," the spokesperson said.
"There are certain areas where we're able to pump the water out, other areas we just have to wait for it to subside.
"The biggest killer at the moment is rain that that keeps coming, but once that rain stops, the rest of the water should subside fairly quickly and we'll be able to get trains through."
The Bureau of Meteorology's Nullarbor weather stations, Balgair and Rawlinna, recorded 69mm and 33mm of rainfall in the past 24 hours, respectively.