The ishihara isn't the the be-all and end-all. If you have questions about it, the Farnsworth Lantern test will have a much higher pass rate, without need of a waiver or a SODA (statement of demonstrated ability).
As TiredSoul mentioned, visit an eye doctor first to discuss your condition.
There are several AME's (aviation medical examiners) who specialize in helping people thorough their medicals with special conditions; money well spent in the long run.
If you can't pass the Ishihara test, the FAA does allow a "light gun" test, involving checking the light signals received from an air traffic control tower. These signals are used to give a pilot information during a time of a radio failure (more of an emergency thing). The signals are red, green, and white light. If you don't pass the light gun test (used to give you a SODA), then you may have a permanent problem on your hands.
There's a test called the Farnsworth Lantern test, which involves a specialized piece of equipment hardly found any more (the Farnsworth Lantern), which has a much higher pass rate, for those with color issues.
An AME in Phoenix used to have two of them. He retired, sold his practice to another physician who continues under the same practice name, My Flight Surgeon. I don't know if he still does the Farnsworth Lantern (FALANT) tests. The FALANT has been replaced with a newer system, called the OPTEC 900.
Pilot Medical Solutions (leftseat.com) offers a referral for those; I believe you can also get it done at certain optometry schools.