It conducts counter illicit trafficking operations, intelligence fusion and multi-sensor correlation to detect, monitor, and handoff suspected illicit trafficking targets; promotes security cooperation and coordinates country team and partner nation initiatives in order to defeat the flow of illicit traffic.
It is associated with the United States Southern Command but is under Coast Guard leadership.
Bill Clinton's Presidential Decision Directive 14 of 3 October 1993 led to a reorganisation of U.S. military anti-drug organisation. On 7 April 1994, Dr. Lee Brown, Director of the Office of National Drug Control Policy, signed the National Interdiction Command and Control Plan which directed establishment of three national interagency task forces (JIATF East in Key West, Florida; JIATF South in Panama; and JIATF West in Alameda, California).
On 1 June 1997, the Commander in Chief U. S. Southern Command expanded his area of responsibility to include the Caribbean and the waters bordering South America, and assumed command and control of JIATF East. In compliance with the 1979 Panama Canal Treaty and the necessity to complete the military drawdown in Panama by the end of 1999, the decision was made to merge JIATF South and JIATF East into one organization. Transfer of the JIATF South mission to the merged JIATF was completed on 1 May 1999.
Due to the previous history of the command, Task Groups 4.1, 4.2, 4.3, and 4.4, and others, are in use controlling U.S. and allied assets assigned to JIATF South. A February 2007 Dutch magazine described the relationships as follows: under the command of the Director JIATF South, the U.S. Tactical Commander held the position of Commander Task Group 4.1, United States Air Force forces cTG 4.2, US Navy forces CTG 4.3, the Director of the Netherland Antilles and Aruban coast guards (DKW NA&A), who is always the commander of the Dutch Navy in the Caribbean area (Commandant der Zeemacht in het Caraïbisch Gebied), Commander Task Group 4.4 (CTG 4.4), and US Customs force CTG 4.5.