Network Rail confirmed that flooding near Slochd had caused cancellations and delays to services from Inverness to Edinburgh and Glasgow, with the line closed between Carrbridge and the Highland capital.
Further delays were expected as a flood warning remains in place for the area, with more rain forecast and the levels of local rivers expected to rise.
Operator Scotrail have urged customers to make their own travel arrangements when travelling from Inverness to Scotland's two largest cities, due to a lack of replacement busses available.
They also confirmed ticket acceptance was in place with City Link busses between Inverness and Glasgow.
A passenger told the Scotsman: ""All trains going south from Inverness cancelled because of flooding. Replacement bus has now broken down half way to Aviemore.
"The river at Carrbidge is the most torrential I’ve ever seen it. It’s taken 2.5 hours to get the 30 miles to Aviemore.
Scotrail said fallen trees on the line between near Perth caused delays to service from Edinburgh and Glasgow to Aberdeen and Dundee, while elsewhere in the North East, services between Keith and Elgin were delayed due to further flooding.
Disruption was also caused to the Caledonian Sleeper service from Euston to Inverness, which terminated at Aviemore, where passengers would be able to continue their journey to Inverness by road.
Network Rail also confirmed that a 10m section of the West Highland Way has been washed away.
We reported yesterday that the West Highland Line would be closed for at least a week as engineers battled to repair sever damage to ballast.