| Original agency | Original department | New agency or office after transfer |
| Customs Service | Treasury | Customs and Border ProtectionU.S. Immigration and Customs Enforcement |
| Immigration and Naturalization Service | Justice | Customs and Border ProtectionU.S. Immigration and Customs EnforcementU.S. Citizenship and Immigration Services |
| Federal Protective Service | General Services Administration | Management Directorate |
| Transportation Security Administration | Transportation | Transportation Security Administration |
| Federal Law Enforcement Training Center | Treasury | Federal Law Enforcement Training Center |
| Animal and Plant Health Inspection Service(part) | Agriculture | Customs and Border Protection |
| Federal Emergency Management Agency | none | Federal Emergency Management Agency (FEMA) |
| Strategic National Stockpile | Health and Human Services | Originally assigned to FEMA, but returned to HHS in July 2004 |
| National Disaster Medical System | Health and Human Services | Originally assigned to FEMA, but returned to HHS in August 2006 |
| Nuclear Incident Response Team | Energy | Responsibilities distributed within FEMA |
| Domestic Emergency Support Team | Justice | Responsibilities distributed within FEMA |
| Center for Domestic Preparedness | Justice (FBI) | Responsibilities distributed within FEMA |
| CBRN Countermeasures Programs | Energy | Science & Technology Directorate |
| Environmental Measurements Laboratory | Energy | Science & Technology Directorate |
| National Biological WarfareDefense Analysis Center | Defense | Science & Technology Directorate |
| Plum Island Animal Disease Center | Agriculture | Science & Technology Directorate |
| Federal Computer Incident Response Center | General Services Administration | US-CERT, Office of Cybersecurity and CommunicationsNational Programs and Preparedness Directorate (now CISA) |
| National Communications System | Defense | Office of Cybersecurity and CommunicationsNational Programs and Predaredness Directorate |
| National Infrastructure Protection Center | Justice (FBI) | Office of Operations CoordinationOffice of Infrastructure Protection |
| Energy Security and Assurance Program | Energy | Office of Infrastructure Protection |
| Coast Guard | Transportation | Coast Guard |
| Secret Service | Treasury | Secret Service |