The discovery was reportedly made a few hours after Boroh was arrested on Monday by a combined team of EFCC and ONSA operatives.
Boroh was also the Coordinator of the Presidential Amnesty Programme.
The anti-graft agency was said to have recovered the money, in conjunction with the Office of the National Security Adviser (ONSA).
According to ThisDay, the discovery was made a few hours after Boroh was arrested on Monday, March 19 by a combined team of EFCC and ONSA operatives.
The spokesman for the EFCC, Wilson Uwujiaren, confirmed Boroh's arrest.
A senior security officer also confirmed that the ex-presidential aide was picked up from his home in Gwarinpa, Abuja on Moinday but was taken back to his residence at about 3 a.m. Tuesday for a thorough search.
It was during the ransacking of Boroh's home that the $9 million was found.
"The former adviser was driven to his home in an unmarked car after his arrest. His home was searched for several hours and about $9 million cash was discovered in several safe boxes in several parts of the house.
"The combined team of EFCC and the National Security Adviser operatives were very thorough with the search. Indeed, at a point, the operatives broke all the locks in the home including his wife’s closet. The recovered cash has been deposited at the Office of the NSA," the security source told ThisDay.
Last week, Buhari announced the dismissal of Boroh and appointed Professor Charles Dokubo as his replacement.
The President also directed the NSA, Maj.-Gen. Babagana Monguno (rtd), to probe the activities of the Amnesty Office from 2015, when Boroh was appointed, especially allegations of financial impropriety and other acts that were allegedly detrimental to the objectives of the Presidential Amnesty Programme.
However, the cash discovered in Boroh's home is one of many cash discoveries made by the EFCC in the last two years.
In April 2017, the Commission uncovered $44.3 million cash at an apartment in Osborne Towers, Ikoyi, Lagos.
Within 24 hours of that discovery, the National Intelligence Agency (NIA) laid claim to the cash, saying that the apartment was used as a safe house for its operations in the South-west.
The discovery eventually led to the sack of the NIA director general, Ambassador Ayodele Oke.