Around 90 per cent of the old building went up in smoke despite prolonged efforts by around 50 firefighters, who rushed to try and save the Royal Deeside landmark.
But fire crews managed to arrive in time to safeguard a replica of the railway carriage once used by Queen Victoria to travel between Windsor and Ballater.
Scottish Fire and Rescue Service said that an investigation into the cause of the fire had been delayed due to the “unsafe nature of the building”.
It is expected investigators may try to gain entry to the property tomorrow.
The Ballater station was opened in October 1866 by the Great North of Scotland Railway and was the nearest station to Balmoral Castle - the Queen’s Scottish holiday home.
The station was believed to be the largest wooden building ever built by the railway operators.
It closed in 1966 but it was later re-opened as a visitor centre for tourists to learn about the Royal Family’s connection to the area.
The station building survived a major fire several years ago when the former garage next door was burnt to the ground in a blaze.
A local policeman managed to douse some of the flames with a fire extinguisher to stop it spreading from the garage.
The popular attraction contained a restaurant, shop, museum and a Visit Scotland information centre.
It is the second time the owners of the Station Restaurant, Nigel and Fiona Franks, have been hit by fire over the past three months.
The couple are still counting the costs of a major blaze which swept through the nearby Darroch Learg Hotel in the village in February.