The Center For Drug Evaluation And Research (CDER) is responsible for warning letters used for pharmacy compounding issues.  See the July 2012 Regulatory Procedures manual found here.  The manual provides the following information guidance:

The Compliance Management System (CMS) is now being used for electronic submission of Warning Letter recommendations from district offices. All recommendations by the district offices must use CMS for submitting the proposed Warning Letter, the FDA 483 supporting alleged violations, the EIR, and any written response by the firm. For any questions, or if you need to submit a document as a hardcopy, the CDER contact is: Director, Division of Domestic Drug Quality, 301-796-3255, fax 301-847-8743. Also, see Exhibit 4-1, the agency’s “Procedures for Clearing FDA Warning Letters and Untitled Letters.” All agency components responsible for issuing Warning Letters and Untitled Letters must follow these procedures.