Submit the report as you were trained to do.  Your supervisor can not alter company policy and I believe here that she may be setting you up for a write up as to procedure (i.e., that you failed to follow procedure here) and that you should make sure that you follow everything by the book and document that you have done so.  By that I mean follow up with e-mails regarding what you have done and note where in the manual or training course material the procedure as you followed is located.  Become the "model" employee.  And if you have a grievance then go to your Human Resources Department.  In other words, follow protocol.  Now, if you believe that they are doing something illegal that is completely different.  Consult with an attorney about going to the Attorney General's Office or the DA.  Good luck to you.