He headed the Research and Analysis Wing (RAW) from December 2014 for a fixed two-year period.
The Appointments Committee of the Cabinet, headed by Prime Minister Narendra Modi, has approved the appointment of Rajinder Khanna as the Deputy NSA on re-employment and on contractual basis, according to the order issued by the personnel ministry.
Rajinder 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.
Mr Khanna is at present Officer on Special Duty (Neighbourhood Studies) in the National Security Council Secretariat.
Neighbourhood Studies prepares policy papers of neighbouring countries including Pakistan, Sri Lanka, Bangladesh and Nepal.
The National Security Council, headed by the Prime Minister, is the top body on all internal and external security-related matters. National Security Adviser Ajit Doval is its secretary.
It is for the first time when both the NSA the and Deputy NSA are from intelligence agency background.
Ajit Doval, a former Indian Police Service officer, retired as chief of Intelligence Bureau, country's internal intelligence agency, in January 2005.
The post was lying vacant since Arvind Gupta, a former Indian Foreign Service (IFS) officer, completed his tenure in August last year. Mr Gupta was appointed to the post in August 2014.