No-one was injured when the non-passenger train came off the tracks at around 5pm on Wednesday, but the incident has had a major impact on travel.
A bus replacement service is in operation while the train is removed and checks are carried out on the line, with ScotRail warning the suspension will continue until at least 6pm on Thursday.
The train operator said: “Engineers are on site at Stonehaven, and will begin work to rerail the train as quickly as possible.
“Once this has been done, Network Rail will also need to inspect the track for damage and make any repairs necessary.”
Other services affected by the incident include the Caledonian Sleeper between Aberdeen and London Euston, and LNER trains between Aberdeen and Leeds/London Kings Cross.
Network Rail said: “Due to a derailment at Stonehaven, there are no trains travelling north from Dundee.
“On conclusion of an investigation, the train will be removed and any damage to the track will be assessed and repaired before service can resume.
“Contact your train operator for alternative travel information.”
Meanwhile in Argyll and Bute, a 60-mile road diversion route is still in place as work continues to make the A83 safe at the Rest and Be Thankful following a landslip.
Operators closed the route on Tuesday morning after around 2,500 tonnes of debris reached the catch-fences above the road following heavy rain.
Bear Scotland said it is concerned about large boulders at risk of slipping further down the slope on to the road.