Deputy National Security Advisor Nehchal Sandhu, a former Intelligence Bureau director, resigned Thursday due to "personal reasons", the government said.
Prime Minister Narendra Modi has accepted the resignation with "regret and expressed appreciation for Sandhu's outstanding service to the country in a career spanning over 40 years", an official statement said.
A career police officer, Sandhu was also the Secretary, National Security Council Secretariat.
Sandhu headed the Intelligence Bureau in 2010-12, and was highly regarded for his contribution to India's fight against terrorism.
Some in the security establishment described Sandhu as a successful clandestine operative and a brilliant analyst.