Watch a report by ITV News reporter Rebecca Barry
The passenger who died in the Stonehaven rail crash was 62-year-old Christopher Stuchbury from Aberdeen, Police Scotland said.
The family of Mr Stuchbury have said they were "devastated by his death".
A statement released by Police Scotland said: "Chris was a much adored husband, son, dad, stepdad, granddad, brother and uncle and was a treasured and loved friend to many, including the Targe Towing Team where he was an integral and valued member of staff.
"He also volunteered at Roxburghe House in Aberdeen during his spare time which he thoroughly enjoyed doing.
"We are devastated by his death and we request privacy at this difficult time as we come to terms with our loss."
Michael Matheson was in Stonehaven on Thursday and praised the response of emergency services in dealing with the incident.
Also at the site of the crash, Transport Secretary Grant Shapps said his heart goes out to the friends and family of the people involved and that "we absolutely must make sure we learn every possible lesson."
The Transport Secretary told ITV News the scene of the incident was "absolutely horrendous" and "difficult to look at".
Mr Shapps said: "I went up in the helicopter and flew over the site and to see what we've got there - with the pictures that people will have seen in the newspapers - through your own eyes is just extraordinary."
Officials have pledged to find out what caused the train to derail near Stonehaven, killing three people and injuring six others.
Mr Matheson claimed adverse weather was increasingly having an impact on routes and the Rail Accident Investigation Branch (RAIB) probe into the incident would reveal whether mitigation works needed to be increased.
ITV News Correspondent Rebecca Barry reports from Stonehaven
Mr Matheson said: “We’ve already experienced significant disruption to the Scottish rail network as a result of these localised, intense weather events.
“They (Network Rail) are well aware of our views about the need to make sure that we are taking forward the right types of mitigations that help to manage a challenge of these types of localised, intense weather events.
“I think one of the things we will see what comes from the investigation is whether the pace of that type of mitigation work needs to be stepped up, that’s not just a challenge across Scotland, it’s across the whole of the UK.
“I think it would be reasonable to presume, without unduly speculating, that weather had an impact in this particular incident.”
A view of the scene in Aberdeenshire
Network Rail chief executive Andrew Haines said: “I will not pre-empt the outcome of the investigation into this awful event, but it is clear the weather was appalling and there were floods and landslips in the area."
Network Rail announced it will carry out “supplementary specialist inspections” of “higher risk” trackside slopes with similar characteristics to the site of the train crash.
Mr Shapps said "there is clearly a concern" around the potential for accidents given flash flooding.
Grant Shapps: 'This may have been some sort of freak accident, we don't know yet, we do need to know'
The 6.38am Aberdeen to Glasgow Queen Street service crashed near Stonehaven on Wednesday morning amid heavy rain and flooding.
Network Rail said there would be a “few dozen” sites where inspections would be needed. They will be carried out by its own engineers, specialist contractors and a helicopter survey will also be used.
It is also talking to weather forecasters to try to get quicker information on flash flooding caused by “unpredictable extreme weather”.
Among the dead were the train’s driver, named as Brett McCullough, as well as the conductor, Donald Dinnie, and a passenger.
The Scottish Fire and Rescue Service also said four firefighters were injured while dealing with the derailment.
The Queen, Prime Minister Boris Johnson and Scottish First Minister Nicola Sturgeon have led tributes to those killed in the “tragic” incident.
A union official said colleagues “thought the world” of Mr McCullough, 45, who leaves wife Stephanie and three children, two girls and a boy.
He is a former gas engineer who had been a train driver for seven years.
Colleagues said he was servicing the gas boiler of an Aberdeen train driver when they started chatting about the job and he decided to join the railways.
Kevin Lindsay, Scotland organiser for the train drivers union Aslef, said: “The tragic accident at Stonehaven has affected everyone in the railway family. Brett thought the world of his family, and his colleagues thought the world of him.”
Dozens of emergency service vehicles – including an air ambulance and British Transport Police (BTP) officers – were called to the scene at about 9.40am.
Of the four firefighters injured, two attended hospital as a precaution and two remained on the scene.
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At her daily coronavirus briefing, First Minister Nicola Sturgeon said the news of the deaths of three people in the Stonehaven derailment was “devastating”. She added that lessons should be learned from the accident, and said her thoughts were with those who work on Scotland’s railway.