99401 represents a preventive service, in other words the patient has no documented disease or condition that requires or would benefit from the nutrition counseling, but is receiving this service only to maintain health and prevent problems from potentially developing in the future. If that is the case with your patient, then this is the correct code and it is in fact a non-covered service under Medicare. It would not be correct or appropriate to bill this as an office visit E&M service if that is not in fact the service that was provided.
If, however, the patient does have conditions or risk factors that would make nutrition therapy a covered condition under Medicare, then those should be billed with the appropriate covered CPT/HCPCS codes, e.g. 97802-97803 or G0270-G0271 as applicable. You may want to take a look at these codes and see if one of them might be more appropriate to the services that were provided. There is also a NCD published by Medicare and guidance in the Medicare Manuals which indicates in which situations nutrition therapy is covered by Medicare plans and how it should be billed.