The 90ft vessel had recently changed hands and was about three-and-a-half years old. It was undergoing a re-fit and re-name, from Amethyst.
It is thought foreign crew members sometimes sleep on the boats in the harbour.
Grampian Fire and Rescue Service's David Rout told BBC Scotland at the scene: "Fire crews encountered an extremely demanding and hazardous situation.
"They were subject to intense fire and heat and there were conditions on the vessel which hampered the operation.
"Our search and rescue teams located three fatalities on board the vessel."
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Investigators board the Vision II trawler
He said a joint investigation was being carried out with Grampian Police.
Six appliances were at the scene, including two from Fraserburgh, two from Peterhead, one from Macduff and one from Maud.
Firefighters used breathing apparatus and thermal imaging cameras as they tackled the flames.
Coastguard and lifeboat teams also went to assist.
Grampian Police said the blaze, which was brought under control by about 0330 BST, did not appear to be suspicious.
Banff and Buchan MSP Stewart Stevenson said: "Obviously my thoughts go out to the friends and family of those who have died.
The prawn trawler was being renamed from Amethyst
"I am sure the police, the fire and rescue service and the appropriate authorities will look very closely at the circumstances surrounding this and I hope we have a speedy understanding of what caused this tragedy."
Bertie Armstrong, chief executive of the Scottish Fishermen's Federation, said: "The fishing industry will be highly concerned.
"There will be heartfelt sympathy for the families of the people involved who have died. We will urgently want to find out what happened.
"Nothing can be done for these three people who died and the question now is how did this happen and how can we avoid this happening again?"
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