The 40-foot Runagate arrived at West Harbour, Granton, at the end of November but the vessel broke moorings in the high winds of Storm Arwen just days later.
Members of the Forth Corinthians Yacht Club helped pull the yacht to safety after the storm struck but the vessel, which is more than 80 years old, has been taking in water and is now back on its side.
The vessel has long held a place in the imagination of Shute fans who embarked on a search for the yacht several years ago, tracking it down to a harbour in Newcastle where its owner lived on board with his parrot.
The yacht was on its way from Berwick-Upon-Tweed to Charlestown in Fife when it moored up in the capital, with it now unlikely to sail again.
Retired IT worker Jim Glass, 65, from Granton, Edinburgh, chair of the Wardie Bay Residents' Association and yacht club member, said: "It's of great historical interest to a lot of people.
"It was in quite bad nick beforehand, frankly. Now, with it being under the water at every tide, and being bashed against that rocky corner of Granton Harbour, I don't think it's going to last long, it'll start breaking up.
"When the tide comes in all you can see is the masts sticking out of the water."
Shute, an English aeronautical engineer of note, became one of the world’s best selling authors during the 1950s with his works including On The Beach and A Town Called Alice, the latter made into a film starring Gregory Peck and Ava Gardner.
The author, who was also known for his adventuring lifestyle, featured a yacht called Runagate in his 1924 book Pilotage with the writer giving his new yacht the same name in 1939.
The boat was designed for him at Hillyards at Littlehampton, West Sussex, following the sale of his aircraft design company Airspeed, with the writer and his wife planning to take an extended holiday.
But as war was declared, Shute returned to aeronautics and became involved in secret weapon development as Great Britain sought a technological advantage over Nazi Germany and its allies.
Later, he moved to Australia with his family with the boat then moving around different homes in the UK, with Edinburgh seemingly the Runagate’s last mooring.
Mr Glass added: “When Storm Arwen hit, it broke free, unfortunately and ended up in one of the corners of the harbour.
"It got a bit of bashing. It was rescued by some of the members of our boat club who tied it up to the wall on Saturday morning.
"They had to physically drag it along.
"When the owner came back he moved it along to a set of ladders but it was damaged so badly it was taking in water. I think it's finished."