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If you have a 2012/2013 HCPC Coding book go to the Index Table Of Drugs, Depo-Medrol, dosage and it references you to the HCPC code, x however many units was administered. You can go two routes you can use J1020-20mg x 1 plus J1030 40mg x 1 or simply J1020-20mg x 3 units. Hope this help.
My thoughts are that you would indeed have to report the NDC code with what was supplied. Just make sure it is current to the DOS you are using as that can cause issues. The NDC codes do change periodically and one has to stay on top these!