According to the Roof Coatings Manufacturers Association, rust on galvanized roofs generally appears in white or red colors. White rust often gives the metal roof a chalky appearance. White rust is the first stage of corrosion in the galvanized metal roof -- red rust indicates that the rust has been ongoing for some time. Once rusting reaches the red phase, the roof will continue to corrode until the rust itself is removed, so consider removal methods regardless of the color of the rust.
If the rust on your galvanized roof is still white, use a solvent-based or water-based rust preventative primer to seal the entire affected area of the roof -- such a primer will generally stem rusting before it reaches the red stage, so long as it is applied properly. Removing red rust is a bit more involved, typically requiring power washing, sand blasting or wire brushing. After the rusted areas have been removed, seal the roof with the same type of sealant described above to prevent future rusting.
To avoid rust problems on your galvanized metal roof altogether, consider one of several preventative roof treatments available. The coatings, when applied to the galvanized metal roof using an aerated sprayer, can prevent rust from forming entirely. In some cases, applying several coats of the treatment will only increase the product's rust prevention power. Always follow the manufacturer's recommended application instructions provided with the product you purchase.
If a large majority of the surface area of your roof is covered in rust, it is always a better option to replace or repair the roof rather than attempting to remove the rust. Removing rusting from a large area of the roof surface is cost inefficient. More importantly, substantial rusting can compromise the structural integrity of the roof, rendering it unsafe to stand on. In these instances, keep people off of the roof until it can be fully repaired.