Question: Must we bill all patients at the same rate? Answer: Technically, no, you don't have to bill all patients at the same rate. As long as you are following a contract or have consistent nondiscriminatory billing policies in writing, billing may vary from payer to payer. Just be sure to keep your billing policies consistent to avoid accusations of discrimination.
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In practice, however, you cannot charge more to Medicare patients than you charge to other patients. If you offer a lower rate for any given service or procedure to non-Medicare patients, you must offer the same rate to Medicare patient.
In fact, many payers (not just Medicare) specify a -most favored nation- clause in their contracts that requires you to charge them no more than you charge anyone else. You should consider all of your contracts, not just Medicare and Medicaid, when determining whether to have multiple fee schedule.