The Picton - Christchurch railway line is closed by slips, flooding and debris.
Ontrack says a slip in the Buller Gorge has also closed the Stillwater - Westport Line, which will affect coal trains.
The Palmerston North - Gisborne line remains closed because of flooding and slips.
Fallen trees have been cleared from the North Island main trunk line in the Levin area and services are operating normally.
Interislander ferries are still sailing.
Commuter rail services in Auckland and Wellington are running without major disruption.