Junaid Abdullahi, a retired pilot, assumed duties at the agency on a low-key on October 18.
He was married to Zulaihat, Mr Buhari’s first daughter who passed away in 2012 from childbirth complications. She was 40.
Mr Abdullahi took over from Jummai Idakwo, the former director of the agency.
Such appointments are usually announced by either the Presidency or the Office of the Secretary to the Government of the Federation.
It was not immediately clear why both institutions kept a sealed lip over the appointment.
A government source who learnt about the appointment last month said it might have been hushed to save Mr Buhari the trouble of again being accused of nepotism.
His critics often raise concerns about how most key federal appointments, especially top national security positions, have been ceded to northerners.