Hill House in Helensburgh faces a significant threat from longstanding issues with "excessive water ingress", the trust said.
The house, built for publisher Walter Blackie in 1902, is regarded as the architect's finest domestic building.
Mackintosh also designed nearly everything inside the house.
NTS, the heritage body which has cared for the building for more than 30 years, said Mackintosh made use of "innovative" building techniques to create the beautiful, minimalist exterior design.
Because he did not use "traditional weathering details", however, there had been "excessive water ingress" into the 113-year-old building.
Director of Conservation Terry Levinthal said the NTS had agreed a strategy for repairing the building and was now beginning a fundraising drive, with an appeal to international donors as well as UK benefactors and grants.
He said: "The Hill House is clearly a place of the highest cultural significance, and must be well looked after.
"Caring for our heritage can be very complex and this project is a prime example of that.
"The trust has been exploring how best to resolve the longstanding issues of water ingress. We have now concluded what our repair strategy is going to be, after considerable research investigation and consultation with stakeholders.
"This is time-consuming and, of course, the costs are significant too.
"We are in the early stages of fundraising in support of this major project to protect the Hill House, Mackintosh's finest example of domestic design, for future generations."
The National Trust for Scotland is trying to raise £2.5m to protect one of Charles Rennie Mackintosh's finest buildings from the weather.