Investigators were seeking answers Thursday over why a train derailed in northeast Scotland, killing the driver, conductor and a passenger.

Smoke rises over derailed carriages at the scene of a train crash near Stonehaven in northeast Scotland on August 12, 2020. (Photo: AFP)

The 06:38 am passenger service from Aberdeen to Glasgow came off the tracks on Wednesday morning near the town of Stonehaven, which had been hit by flooding following heavy rain.

Six people were hospitalised with minor injuries and police said the train had fortunately not been busy, with media reports saying just 12 people were on board.

Aberdeen is subject to tighter coronavirus restrictions than the rest of Scotland due to a localised outbreak of COVID-19, with people advised not to travel to the city.

Government ministers were due to visit the site on Thursday and investigators are already picking through the debris, including the ashes of a fire that left four firefighters with minor injuries.

A landslip had been reported close to where the train derailed at 09:43 am (0843 GMT), and Prime Minister Boris Johnson was among those to suggest the weather might have played a part.

"It's probably a very good idea to look at the effect of substantial rainfall on all our vulnerable infrastructure everywhere," he told Sky News on Wednesday.

"And as I understand there was about a month's worth of rainfall in a very short period which undoubtedly aggravated the problem there."

However, he said it was up to investigators to determine what caused Britain's first major derailment for 13 years and vowed to "make sure nothing like this happens again".

Queen Elizabeth II, who is staying in her Scottish home of Balmoral around 50 miles away from Stonehaven, sent her condolences.

Scotland's Transport Secretary Michael Matheson said he would meet members of the emergency services in Stonehaven, saying they had faced "significant challenges" at the site.

He told BBC Radio Scotland that changing weather patterns posed difficulties across the railways.

"The rail networks are experiencing increasing challenges across different parts of the routes, not just here in Scotland but across the UK, due to what is an increasing number of very intense localised weather events that have a significant impact on the infrastructure," he said. 

Britain's last major rail derailment was in 2007 in Cumbria, in northwest England, which left one passenger dead and 30 others injured.