The NIA was formed in 1994 following South Africa's South Africa's first multi-racial elections. It was created to take over from the domestic intelligence segment of the then National Intelligence Service (NIS) with the foreign intelligence functions being taken over by the South African Secret Service (SASS). Both the SASS and NIA were created as part of the Intelligence Act of 1994. As of October 2005, the head of the NIA was Manala Manzini.
The NIA has received some media attention of late due to media reports of an Al-Qaeda plot to attack targets in parts of South Africa. The NIA investigated the claims and reported them to be false. However, the NIA remains alert to the possible presence of Al-Qaeda operatives in the country, and in April 2004 a number of alleged operatives were arrested and deported. The NIA works closely with the Crime Intelligence Division of the South African Police Service in this regard.