The post was lying vacant since Arvind Gupta, a former Indian Foreign Service (IFS) officer, completed his tenure in August last year. Gupta was in August 2014 appointed to the post.
Khanna, a 1978 batch Research and Analysis Wing Service (RAS) officer, has supervised several counter-terrorism operations and is considered an expert on Pakistan and Islamic terrorism.
The Appointments Committee of the Cabinet headed by Prime Minister Narendra Modi has approved the appointment of Khanna as Deputy NSA on re-employment and on contractual basis, the order issued by personnel ministry said, without mentioning his tenure.
Neighbourhood Studies prepares policy papers of neighbouring countries including Pakistan, Sri Lanka, Bangladesh and Nepal.
The National Security Council, headed by Modi with National Security Adviser Ajit Doval as its Secretary, is the apex body on all internal and external security-related matters.
It is for the first time when both the NSA the and Deputy NSA are from intelligence agency background.
Doval, a former Indian Police Service officer, retired as chief of Intelligence Bureau, country's internal intelligence agency, in January 2005.
Doval was India's main negotiator with the hijackers of the Indian Airlines plane IC-814 that was taken to Kandahar in Afghanistan in 1999.
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