Trains south of Timaru are operating, as are trains running into Christchurch from the north – as well as in the Garden City's metro area.
However, the Midland Line from Christchurch to the West Coast has also suffered significant damage.
Moyle said there are "a number of sites" where the track has been washed out – with up to nine sections that need urgent repairs.
He believes it could be another three to four days before the Midland Line is open.
The Ashburton River/ Hakatere road bridge was closed this morning after drivers reported slumping at the Ashburton end.
Waka Kotahi NZ Transport Agency engineers have been inspecting the bridge and its piers today.
"We need to understand the degree of damage before we can look at a repair strategy and possible timeframes for reopening the bridge," Waka Kotahi journey manager Tresca Forrester said.
There is no detour via road currently open.
But Prime Minister Jacinda Ardern, who was given a helicopter tour of the region's flooding today, said the "major focus for us is to get the transport links back up and running".
"Work is underway as we speak to try and reinstate some of those alternative routes," Ardern said.
"We've been advised that those should be reinstated by the end of today, but extensive work needs to happen in order for that to be successful."
Shoppers at Foodstuffs stores could see some empty shelves south of Ashburton today, head of corporate affairs Antoinette Laird said.
The company faced "delivery challenges" to southern stores due to the road closures in the region.
"Customers might see some gaps on shelves until our trucks can get through to make deliveries," Laird said.
"Foodstuffs South Island is well used to dealing with extreme weather events, so we ask all customers to please shop normally to avoid putting unnecessary stress on stores."
A Countdown spokeswoman said the company was facing similar issues as lower South Island deliveries had been affected by flooding.
