The EFCC agents allegedly recovered $9.2million from Yakubu’s safe and an additional £72,000.
The anti-graft agency said that it was the largest amount they had recovered in recent weeks.
Yakubu was arraigned in June 2016 on allegations of money laundering.
He served as GMD of NNPC between 2012 and 2014, during the Goodluck Jonathan regime.
He was sacked by the then Minister of Petroleum Resources, Diezani Alison-Madueke, who reportedly accused him of insubordination.