The fire broke out in the NHS Highland property on Sunday morning.
Fire crews from Inverness, Fort Augustus, Foyers and Drumnadrochit tackled the blaze. Firefighters remained on the scene for three hours.
Scottish Fire and Rescue Service (SFRS) said the cause of the fire was not believed to be suspicious.
A temporary doctors' surgery has been set up in a Church of Scotland manse in Fort Augustus after a fire badly damaged the village health centre.