Emergency services attend the scene of a derailed train in Stonehaven, Scotland, on Wednesday. AP
"Very sadly despite the best efforts of paramedics, we can confirm that three people have been pronounced dead at the scene," British Transport Police said in a statement.
Police, several ambulances, an air ambulance and fire engines were at the scene.
Helicopters and police vans are pictured near the scene of a train crash by Stonehaven in Scotland. AFP
Transport Secretary Grant Shapps told the BBC authorities were "still waiting for a clearer picture” about how many people had been injured and "lost their lives as well.”
The British Transport Police force said officers were called at 9:43am to the railway line near Stonehaven, about 160 kilometres northeast of Edinburgh.
Local lawmaker Andrew Bowie said Aberdeen Royal Infirmary had declared a major incident. Bowie had been in Stonehaven surveying flood damage earlier on Wednesday.
"The situation was really bad this morning. The River Carron, the main river which flows through it, had burst its banks, and the heavy rain had caused flooding in the center of Stonehaven and lots of the side streets leading off it,'' he said.
Emergency services attend the scene of a derailed train in Stonehaven. AP
Bowie added that the water had receded and it was unclear if flooding was connected to the derailment.
"I don’t think speculation is helpful at this stage,'' he said. "We obviously don’t know why the derailment took place, but obviously we have suffered terrible weather here.”
Stonehaven is on the line for passenger trains linking Aberdeen with the cities of Edinburgh and Glasgow. The hilly area was hit by storms and flash flooding overnight.
Serious train accidents are rare in the UK The country's last fatal derailment was in 2007.
The head of Network Rail cut short a family holiday in return to the UK.
Prime Minister Boris Johnson tweeted: "I am saddened to learn of the very serious incident in Aberdeenshire and my thoughts are with all of those affected. My thanks to the emergency services at the scene.”
President His Highness Sheikh Khalifa Bin Zayed Al Nahyan has sent a cable of condolences to Abdel-Fattah Al Sisi, President of Egypt, for the victims of the collision between two passenger trains.
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Iranian state TV reported that rescue teams were dispatched to the quake-hit area and added there were no casualties.
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