The rail line between Ashburton and Washdyke will be out for at least another week after this week's flood damage.
KiwiRail teams are also busy clearing slips on the Midland line, which links Christchurch and Greymouth, with it expected to re-open next week.
South Island operations manager Mark Heissenbuttel said the damage to the line between Ashburton and Washdyke was more severe and cost assessments are still being done.
A massive clean-up is under way across the wider Canterbury region after a one-in-100-year weather event dumped torrential rain, causing rivers to burst their banks and forcing the evacuation of hundreds of homes.
Heissenbuttel said there was a large amount of work that needed to be done yet to repair three bridges, clean up washouts and remove debris.
The Main South Line from Christchurch to Ashburton reopened yesterday.
Prime Minister Jacinda Ardern was given a helicopter tour of the region's flooding earlier this week.
She said the "major focus for us is to get the transport links back up and running".