First, it depends on how much color deficit you have. If you cannot pass the color plates (Ishihara, Keystone vision tester, Titmus vision tester, Dvorine plates) and he does not have a Farnsworth Lantern (FALANT) you will be issued a restriction for night flying and flying with signal light guns.
If this occurs, you can take a FALANT (see
http://www.myflightsurgeon.com ) and if you pass request a letter of evidence for color vision from the FAA.
Your final course of action is to request a light gun test from the FAA. If you do this, you get only 2 tries in a lifetime.
The color vision standards are the same for all 3 classes of medical certificate.