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.

FDA Division of New Drugs and Labeling Compliance

The FDA Regulatory Procedures Manual Dated July 12 (found here) defines the responsibilities of the Division of New Drugs and Labeling Compliance.  Note that number 7 and 8 appear to be identical.

1-4-2 Division of New Drugs and Labeling Compliance
The division’s primary responsibility is to protect the public health by ensuring compliance with the new drug and misbranding requirements of the Federal Food, Drug and Cosmetic Act as it relates to over-the-counter (OTC) drugs, prescription (Rx) drugs, and drugs falling within the health fraud program area.
The division consists of five teams, the Over-The-Counter Drugs Team, the Internet and Health Fraud Team, the Pharmacy Compounding Team, the New Drugs and Labeling Team, and the Import-Export Team. The functional statements for the Division of New Drugs and Labeling Compliance are:
1. Protects the public health by assuring compliance with the new drug and misbranding requirements of the Federal Food, Drug, and Cosmetic Act as it relates to over-the-counter (OTC) drugs, prescription (Rx) drugs, and drugs falling within the health fraud program area;
2. Develops compliance strategies, programs and policy guides to ensure that all OTC and Rx drugs marketed in the United States are properly labeled and meet applicable new drug requirements and to remove from the market fraudulent drug products that pose direct or indirect public health risks;
3. Maintains the integrity of imported drug products by assuring their compliance with applicable legal requirements;
4. Provides guidance and consults on export policies and procedures;
5. Directs field inspections and investigations and recommends, directs and/or coordinates case development and compliance actions regarding OTC, Rx, and health fraud drug products;
6. Provides enforcement and litigation support and guidance for OTC, Rx, and health fraud drugs, including support for State Attorney General and Office of Criminal Investigation cases;
7. Develops legislative proposals, implementing regulations, policy, and guidance documents; enforcement strategies; and outreach activities relating to pharmacy compounding;
8. Develops legislative proposals, implementing regulations, policy and guidance documents, enforcement strategies, and outreach activities relating to pharmacy compounding;
9. Monitors the Internet in support of division enforcement initiatives, actions and outreach programs; and,
10. Prioritizes unapproved drugs identified for regulatory action using risk based assessment and develops compliance strategies to address the most significant legal violations.