Tunde Ayeni was reportedly arrested in Abuja on Thursday and is currently being detained by the anti-graft agency while investigations continue.
The EFCC is investigating claims that about N36.5 billion and $30 million were diverted from Polaris Bank through a network of companies linked to Ayeni.
The money was allegedly obtained as loans meant for specific business projects.
It was gathered that the funds were meant for ventures such as marine security, electricity distribution contracts, and estate development.
However, the money is said to have been redirected into other accounts and used for unrelated purposes.
The EFCC also alleged that part of the money was used to acquire telecom-related assets associated with NITEL/MTEL through a NATCOM account.
The commission is further examining about 12 companies believed to be connected to Ayeni and allegedly used to secure the loans.
Tunde Ayeni is expected to face charges after the investigation is completed.
When contacted, EFCC spokesperson Dele Oyewale confirmed the arrest but did not give additional details.
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