Damage to the line is to be reviewed before a decision can be made on its reopening.
ScotRail confirmed disruption was expected on services between Aberdeen and Inverness as a result.
Services from Inverness will terminate and start at Keith while those from Aberdeen will terminate and start from Huntly.
Train tickets are being accepted on Stagecoach Highland and First Aberdeen services.
Owing to heavy rainfall overnight between Linlithgow and Edinburgh Park, a signal fault has also resulted in delays to ScotRail services there.
Services are likely to be delayed by up to 20 minutes in that area.
Earlier this morning, engineers managed to reopen lines at Hartwood which had been hit by heavy rainfall.
More details to follow.
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