Six others were injured in the incident, which left carriages strewn over the track and a power car at one end of the train on fire.
The crash is the first incident involving a fatality on a train since a Glasgow-bound Virgin Trains express derailed in Cumbria 13 years ago, in which one passenger died.
It is understood today’s incident happened after the Inter7City train from Aberdeen to Glasgow had earlier encountered a landslide or flooding after heavy overnight rain.
However, it is yet to be confirmed whether the train continued south or was returning towards Aberdeen when the derailment happened, and how fast it was travelling.
It is also not known where the train was in the three hours between leaving Aberdeen at 6:38am and the incident being reported.
The train had reached Stonehaven, four miles from the crash site, at 6:53am according to a tracking website
BTP said it was called to the line at 9:43am following a report that a train travelling from Aberdeen to Glasgow Queen Street had derailed.
A spokesperson said: “Very sadly despite the best efforts of paramedics, we can confirm that three people have been pronounced dead at the scene.
“While formal identification is yet to take place, the driver of the train is very sadly believed to have died.
"His family have been informed and are being supported by specially trained family liaison officers.
“Officers are continuing to work to inform the families of the other two people who sadly died.
“Six people have been taken to hospital to be treated for injuries, which thankfully are not believed to be serious.”
Chief Superintendent Eddie Wylie said: “This is a tragic incident and first and foremost our thoughts are with the families and friends of those who have very sadly died this morning.
“We remain on scene alongside our emergency service colleagues, and a major incident operation has been underway.
"I would like to reassure the public that this was not a busy service, and from CCTV enquiries and witness statements we believe all passengers have been accounted for.
‘Thorough search will be conducted’
"However, once the area has been made safe then a full and thorough search will be conducted, which is likely to take some time.
“I know many people will understandably have questions, and we will be working closely alongside the Rail Accident Investigation Branch and the Office of Rail and Road to establish the full circumstances of how the train came to derail.”
The Rail Maritime and Transport union (RMT) later revealed a conductor also died, and ScotRail said the third fatality had been a passenger – one of just six believed to have been on board.
Alex Hynes, managing director of Scotland’s Railway, which comprises ScotRail and track owner Network Rail Scotland, said: “Our thoughts are with those who have been affected by this tragic event, particularly the families of those who have lost their lives.
"The railway in Scotland is often referred to as a family, and it’s one that is hurting today.
“We have teams on site and we will do all we can to support everyone affected.
"We are working closely with all the relevant authorities to establish the cause of this incident.”
‘Extremely serious incident’
Earlier, First Minister Nicola Sturgeon told MSPs a major incident had been declared.
She described the derailment as an “extremely serious incident west of Stonehaven”.
The Transport Salaried Staffs Association (TSSA) union said four carriages of the 6:38am Aberdeen to Glasgow Queen Street service had derailed.
The union, which represents engineering and maintenance staff at Network Rail and ScotRail, said the incident happened at Carmont and was reported around 9:45am.
It said the derailment had followed a night of thunderstorms and heavy rainfall.
General secretary Manuel Cortes said: “Our thoughts are with those caught up in this derailment, their loved ones and the emergency services and our members who are now involved in a rescue operation.
“Our union has had concerns about the amount of hours that some of our members who maintain have been doing.
‘Our thoughts are with everyone involved’
"However, it's far too early to speculate whether this may have been a contributing factor to this morning's incident.”
Kevin Lindsay, organiser in Scotland for the Aslef train drivers’ union, said: ‘Our thoughts tonight are with all those who died, and who were injured, in the tragic accident.
"While it is too early to speculate about the causes of the crash, it would seem that the appalling weather conditions in the area – the torrential rain – resulted in a landslip which, in turn, caused the train to derail.
"The train rolled down a steep embankment and caught fire.
‘There will be an investigation into the causes of the crash, and we will learn those lessons, as we have in the past, because the railway is one of the safest modes of transport.
"The UK has some of the safest railways in the world, and Scotland is the safest part of the UK, but that does not, of course, diminish the impact of today’s crash on all those involved.”
Rail journalist Phil Haigh tweeted: “Train derailed was 0638 Aberdeen-Glasgow.
"It stopped south of Carmont having seen a landslip.
"It was returning north, initially on the southbound line, then on the northbound having crossed at Carmont.
"It then hit a second landslip and derailed as it was returning to Stonehaven.”
RMT union senior assistant general secretary Mick Lynch said: "The confirmation that there have been three fatalities in the Stonehaven derailment, including the driver and one of our conductor members, is the most dreadful news and this trade union's thoughts are with the families, colleagues and friends of those who have lost their lives in this tragedy.
"RMT will unite to provide support, assistance and solidarity at this distressing time.
"Safety on the railway has to be an absolute priority and this union will be working with the various agencies to establish the facts behind this disaster which has sent shock waves right throughout our industry."
Scottish Conservative leader Douglas Ross said: “Today's events are heartbreaking and hard to bear.
“Only one conclusion can be drawn from the early reports and images we have seen - this is nothing short of a disaster.
“All our thoughts are with the family and friends of those involved, and I would like to thank the brave emergency services who are dealing with the incident.”
A message from the Editor:
Thank you for reading this story on our website.
While I have your attention, I also have an important request to make of you.
With coronavirus having a major impact on many of our advertisers - and consequently the revenue we receive - we are more reliant than ever on you taking out a digital subscription.
Subscribe to scotsman.com and enjoy unlimited access to Scottish news and information online and on our app.
With a digital subscription, you can read more than 5 articles, see fewer ads, enjoy faster load times, and get access to exclusive newsletters and content. Visit https://www.scotsman.com/subscriptions now to sign up.
Our journalism costs money and we rely on advertising, print and digital revenues to help to support them.
By supporting us, we are able to support you in providing trusted, fact-checked content for this website