Buildings designed by Mackintosh need immediate work if they are to have a future, according to curator, gallery owner and Mackintosh expert Roger Billcliffe.
Although praising some "wonderful success stories" in saving Mackintosh buildings in recent years, Mr Billcliffe said the outlook for others was "not at all rosy".
He told The Herald that the physical state of the building housing the Willow Tea Rooms in Glasgow's Sauchiehall Street was "very worrying", as was the state of Scotland Street School, parts of which he said were in "appalling condition".
One of Mackintosh's most famous buildings, The Hill House in Helensburgh, has "serious problems" with its harling, the covering used to coat the outer walls of the building. He added: "It's going to be expensive to resolve, and while a solution is sought the structure and interiors continue to deteriorate.
"The National Trust for Scotland is between a rock and a hard place here, and it's not entirely fair to criticise them, but they seem to have known of the problem for at least a decade."
The Queen Margaret Medical College, one of the earliest designs by Mackintosh, is in a "pretty terrible state, standing exposed and forlorn", according to Mr Billcliffe. However, he is positive about its recent acquisition by the G1 Group, given the company's good track record of restoring older buildings and finding them a new use.
A G1 spokesman said: "We are undertaking a process of protecting and conserving the building in conjunction with Historic Scotland and other bodies."
Other buildings about which Mr Billcliffe has serious concerns include the Martyrs School – which, like Scotland Street School, is run by Glasgow Life – as well as the former Daily Record building in Renfield Lane, Craigie Hall in Dumbreck, and Mackintosh's masterpiece, the Glasgow School of Art.
Mr Billcliffe notes his concerns in his new book, Visiting Charles Rennie Mackintosh, which is published next month.
Anne Mulhern, who runs the Willow Tea Rooms, said she is well aware of the structural problems with the building, owned by the Wilson Group of Northern Ireland, which is trying to sell it.
She said she had been in consultation with Glasgow City Council and the Charles Rennie Mackintosh Society over the state of the building.
A spokesman for Glasgow Life said: "There is a constant programme of works maintaining the buildings we manage and a refurbishment of the windows to the rear of Scotland Street School Museum is due to finish later this week. We are also starting to plan what part the Charles Rennie Mackintosh items in Glasgow's collection might play in his 150th anniversary in 2018."
A spokeswoman for Glasgow School of Art said work had been carried out recently, with the mix of new and older harling giving the impression of patchiness "but this will reduce with time as the newer harling ages."
Since its completion in 1904, The Hill House in Helensburgh, designed by Mackintosh for Glasgow publisher William Blackie, has suffered from the effects of moisture penetration though its external plasterwork – a cement-based harling applied at the behest of Blackie to give him a house devoid of "adventitious ornamentation".
A National Trust spokeswoman said: "The Trust is currently exploring how best to resolve the longstanding issues of water ingress and the associated damp caused by the cement harling, which at the time of building was relatively untried.
"We have appointed a consultant to carry out a survey and who will look at previous repairs. In the longer term, we do recognise a major project may be needed."