The fire service, police and ambulance service went to the scene near Stonehaven at about 9.40am on Wednesday.
Smoke could be seen billowing from the train on the track in the countryside, while several emergency service vehicles could be seen parked in a field.
The train involved was the 06.38 Aberdeen to Stonehaven, made up of a locomotive and four carriages.
It is understood the locomotive and three carriages derailed and slid down an embankment.
Unions called the crash a “tragedy” as a major incident was declared at Aberdeen Royal Infirmary.
Separate sources told the PA news agency at least one person has died, although that has yet to be officially confirmed.
Speaking before First Minister’s Questions on Thursday, Nicola Sturgeon said although “details are still emerging”, there are “early reports of serious injuries”.
She said: “My immediate thoughts and the thoughts of those across the chamber are with all those involved.”
Local MP Andrew Bowie said he had spoken to the UK’s Transport Secretary Grant Shapps, who is liaising with Network Rail Scotland and ScotRail about the derailment.
He told the PA news agency: “It’s obviously a terrible situation, a train derailment, the emergency services are on the scene.
“I’ve already spoken to Grant Shapps, who has spoken to Network Rail and the British Transport Police, who are obviously investigating and assisting.
“I am aware that Aberdeen Royal Infirmary has declared a major incident.”
Train operator ScotRail posted a message on Twitter shortly after 6.30am warning that services across Scotland would be disrupted due to “extremely heavy rain flooding”.
A video shared on Facebook at 7.30am shows heavy flooding in Stonehaven
A British Transport Police (BTP) spokesman said: “Officers are currently responding to an incident on the line in Stonehaven.
“We were called at 9.43am and are on scene alongside paramedics and the fire brigade.”
A ScotRail spokesman said: “We’re assisting the emergency services with an incident near Stonehaven and will provide more information when available.”
A Police Scotland spokesman said: “A report was received of a train having derailed near Stonehaven at 9.40am on Wednesday August 12.
“Emergency services are currently in attendance and the incident is ongoing.”