According to what I can gather, multiple agencies are responsible for pandemic response during such an emergency, but the Department of Health and Human Services would direct all pandemic response reactions. For example, the Department of Health and Human Services made the HHS Pandemic Influenza Plan in November 2005. While made by the HHS, the plan listed different departments with different roles for fighting the pandemic:
Department of Health and Human Services (HHS)
Secretary of Health and Human Services
directs all HHS pandemic response activities.
Office of Assistant Secretary for Health (ASH) coordinates HHS pandemic activities and monitors progress.
Office of the Assistant Secretary for Public Health Emergency Preparedness(OPHEP)
coordinates HHS response activities with other federal departments and agencies.
National Vaccine Program Office (NVPO)
coordinates development and revisions of the pandemic preparedness and response plan; coordinates and monitors preparedness activities during the inter-pandemic period, reporting to ASH; coordinates HHS agencies on vaccine issues via the Interagency Vaccine Group (IAVG).
Office of the General Counsel (OGC) advises on law related to key pandemic response activities.
Office of the Assistant Secretary of Public Affairs (ASPA)
develops communications plan including public messages and materials.
Office of Global Health Affairs (OGHA) oversees interactions with other governments and international organizations related to pandemic preparedness.
Centers for Disease Control and Prevention (CDC)
works with partners throughout the nation and the world to monitor health, detect and investigate health problems; develops, evaluates and modifies disease control and prevention strategies; stockpiles antiviral drugs and other essential materials; promotes and supports influenza vaccination programs. The Influenza Pandemic Operation Plan (OPLAN) is published by the CDC.
Food and Drug Administration (FDA)
regulates and licenses vaccines and antiviral agents through the Center for Biologics Evaluation and Research and the Center for Drug Evaluation and Research, respectively; develops influenza viral reference strains and reagents and makes them available to manufacturers for vaccine development and evaluation.
National Institutes of Health (NIH)
conducts and supports biomedical research, including vaccine research and development.
Health Resources and Services Administration (HRSA)
oversees the National Vaccine Injury Compensation Program; coordinates planning for health care and hospital surge capacity and emergency preparedness.
Centers for Medicare and Medicaid Services (CMS) promotes and supports influenza vaccination for Medicare patients' fosters improved delivery of influenza vaccination to hospitalized pneumonia patients.
National Vaccine Advisory Committee (NVAC)
is made up of 15 members appointed for rotating four-year terms by the Director of the NVP in consultation with the National Academy of Sciences, from among individuals who are engaged in vaccine research or the manufacture of vaccines; or who are physicians, members of parent organizations concerned with immunizations, or representatives of state or local health agencies or public health organizations. The Committee advises the Assistant Secretary for Health (ASH) on pandemic preparedness from perspectives of the multiple stakeholders including in the committee membership.
Vaccines and Related Biological Products Advisory Committee (VRBPAC)
advises the Commissioner of Food and Drugs in discharging his responsibilities as they relate to helping to ensure safe and effective biological products, and as required, any other product for which the FDA has regulatory responsibility.
Department of Homeland Security (DHS)
has the overall authority for emergency response activities and will coordinate interventions to maintain community services during a pandemic.
Department of Defense (DoD) and Department of Veterans Affairs (VA)
provides surge capacity of medical equipment, materials and personnel when needed during an emergency.
Department of Agriculture (USDA) conducts surveillance for influenza in domestic animals.
Department of Energy (DOE) and Department of Transportation (DOT)
maintains infrastructure during a pandemic.
Department of Interior (DOI)
responsible for ensuring public health on more than 500 million acres of land across the country.