It was also learnt that the cash might have been transferred to the Consolidated Revenue Fund (CRF) account of the Federal Government.
But it was unclear if the cash has been spent or returned to the National Intelligence Agency (NIA) which was the original owner.
Neither the Office of the Minister of Finance and Budget Planning nor the Office of the Accountant-General of the Federation was ready to speak on the issues last night.
An official of the apex bank also declined to comment yesterday. He said customer-bank confidentiality will be respected.
The House of Representatives on Wednesday raised questions about the status of the cash which was recovered by the Economic and Financial Crimes Commission (EFCC).
The Director of Finance and Admin in the Office of the National Security Adviser(ONSA), Brig. General Ja’afaru Mohammed said the office was not in custody of the $43.4m.
The cash was seized in April 2017 from Flat 7B, No. 16 Osborne Road, Osborne Towers in Ikoyi, Lagos.
It was learnt that the intercepted cash was transferred to the CBN vault pending the final forfeiture order by a Federal High Court.
The money was said to have remained in the custody of the CBN until it was finally forfeited to the Federal Government.
A highly-placed source, who spoke in confidence, said: “Upon interception of the $43, 449, 947, 000, it was deposited with the CBN and receipted pending a forfeiture order by the Federal High Court. The CBN has Recovered Funds Account.
“There was no diversion whatsoever. The cash was with the CBN until it was eventually forfeited.
“The House of Representatives should not embark on a wild goose chase. Every movement of the cash was documented.
“From records, about $286million was released to NIA out of which the $43.4million was intercepted in the affected flat.
The source added: “The $1, 658, 000 Flat 7B, No. 16 Osborne Road, Osborne Towers, where the cash was kept has also been forfeited to the Federal Government. Nothing has been done with it.
“I think NIA designed it as a safe house for strategic activities.”
The Director of Finance and Admin in the Office of the National Security Adviser, told the House Adhoc committee that ONSA had nothing to do with the money.
He explained that money recovered from the NIA was about $41 million which has been returned to the agency on the directive of President Muhammadu Buhari.
He said “The operation that was carried out at Osborne Towers Ikoyi Lagos was planned and executed by EFCC operatives. ONSA was neither part of the team that recovered the funds nor were the funds handed over to ONSA at any point of the recovery.
“However, for the avoidance of doubt, there were issues of funds belonging to an intelligence outfit that was taken out of the abode and was later returned to the outfit on the directive of Mr. President. Evidence of the deposit of the fund is hereby attached.
“The NIA was under investigation and the President directed that the ONSA should take charge of the place. I was sent there to take charge of the funds of the agency. I went there and counted the money in their vault and it was about $41million .
“We kept that money and after the investigation, the President ordered that the money be returned to the agency. We have returned it to the owners as directed by the President”.
When asked of the status of the cash, a top official of the CBN told The Nation that the apex bank as banker to the government would not divulge the status of any fund to a “third party”.
According to the official, only a court order or a parliamentary request could compel the CBN to disclose the status of such funds.
The CBN he said will maintain bank-customer confidentiality agreement between it and the government it serves.
The federal ministry said “no comments please”