Mr. Sandhu, a former Intelligence Bureau Director, joined the NSA’s office in March 2013 on a three-year contract. He put in his papers more than 20 months ahead of time.

Deputy National Security Adviser (Deputy NSA) Nehchal Sandhu resigned on Thursday. With two other officials retiring, the secretariat of NSA Ajit Doval has been left with three vacancies.

The tenure of Joint Intelligence Chief Ajit Lal and Military Adviser Lt. General Prakash Menon came to an end on July 31 and they did not receive any extension.

Mr. Sandhu, a former Intelligence Bureau Director, joined the NSA’s office in March 2013 on a three-year contract. He put in his papers more than 20 months ahead of time.

Mr. Sandhu told The Hindu that he had resigned for “personal reasons”.

However, the exit of three senior officers, appointees of the previous UPA government who worked under the then NSA, Shiv Shankar Menon, gave rise to speculation that the government was looking for its own replacements.

While some in the intelligence establishment believe that Arvind Gupta, chief of the government think tank Institute of Defence and Strategic Analysis was being considered as replacement for Mr. Sandhu, other sources said the government was looking closely at Mr. Doval’s own former think tank, the Vivekananda International Foundation.

Principal Secretary to the Prime Minister Nripendra Misra was an executive council member of that foundation and Additional Principal Secretary P.K. Mishra was its senior fellow. Among retired officers now being considered for key advisory positions to the government are former RAW (Research and Analysis Wing) chief C.D. Sahay, former Urban Development Secretary Anil Baijal, retired Air Marshal S.G. Inamdar, former DRDO Director-General V.K. Saraswat, former BSF chief Prakash Singh and former Ambassador Prabhat Shukla.

Mr. Sandhu had been handling several sensitive assignments in the Prime Minister’s Office for the past 16 months, including cyber security and strategic projects such as road and rail links in border areas