How can I fill a small hole in fiber cement siding?
"If you have some small cracks and holes in your siding, you can fill them in with patching material specifically designed for this purpose, available at your local hardware store. Keep in mind that the patching will be obvious, whether or not you paint over it, so this is the best solution if the cracks and holes are in out of the way places that aren’t readily noticeable. If you have really big holes and cracks, then the siding will probably have to be replaced altogether."

Source: http://www.doityourself.com/stry/how-to-repair-fiber-cement-siding#b