It was learnt that the building where the $50m was found had been under EFCC surveillance for a while because of some high-profile tenants.
According to The Nation, the Economic and Financial Crimes Commission (EFCC) was trailing five high-profile tenants in the building when it found the $43.4 million, £27,000 and N23 million at House 6, Apartment 7B.
The building was said to have been under surveillance for a while because of the tenants.
The report said four of the tenants have been quizzed, with a petition pending against the fifth.
Sources told the newspaper that after a whistle-blower alerted the EFCC about the cash-load apartment, its operatives moved in, not knowing that the National Intelligence Agency (NIA) had a Safe apartment there.
It was gathered that the EFCC had been trying to identify the tenants' assets, including choice apartments in the towers.
A source said: "As at the time of the EFCC's operation on Wednesday, about five high-profile tenants, who are either being investigated or on the radar of the commission, were suspected to be living or having apartments there.
"Some of the tenants have been quizzed and others are undergoing investigation. Only one of them has an outstanding petition still being probed by EFCC detectives.
"Among them are two former governors, a director of the Nigerian National Petroleum Corporation (NNPC) and two prominent lawyers.
"So, when the whistle-blower raised the red flag, the EFCC was quick to move in without knowing that the 7B apartment is a safe house of the NIA.
"There was excitement in the Lagos Zonal office of the EFCC about a breakthrough. This was why the operation started between 10am and 11am."
The source also said that the EFCC hesitated to cooperate with the NIA.
Another source, a government official, reportedly spoke about what happened between the EFCC and the NIA.
He blamed the confusion on a communication gap between the two agencies.
He said: "It is unfortunate that this is the second time this type of incident is happening between the two agencies.
"There was a case of some cash released for contingency assignment by presidential fiat through the NIA account. The release was based on the directive of ex-President Goodluck Jonathan.
"When the EFCC began the investigation of some Politically Exposed Persons (PEPs), it traced the movement of the cash to NIA account. "Instead of seeking explanation from the Director-General of NIA, Ambassador Ayo Oke, the EFCC wrote directly to the Central Bank of Nigeria( CBN) to demand the details of the transactions on the said account.
"In fact, the documents obtained from CBN included other sensitive operations and overhead. The NIA took exception to it. When President Muhammadu Buhari intervened, he saw all the records that neither NIA DG nor any staff benefited from the said funds.
"NIA actually transferred the whole money as directed by the ex-President to another dedicated account. Subsequent EFCC investigation did not indict NIA. As for Wednesday’s operation, it was true that DG of NIA rushed to the Acting chairman of EFCC, Mr. Ibrahim Magu, who promised to intervene. The NIA boss only asked EFCC to retrieve the cash without making a public show of it in the media.
"At the time the NIA got in touch with EFCC, the operation was already midway and strategy wise, the EFCC chairman felt it would convey a different impression because a crowd had already gathered in and around the towers."
According to the source, "the operation was based on the clues from the whistle-blower. The commission acted on intelligence. No one gave EFCC a list of safe houses of NIA. And the cash was also considered huge for NIA’s covert operations."
He added that the EFCC secured clearance from a senior intelligence officer before continuing its operation after entreaties from the NIA.
"I think there was communication gap somewhere and lack of synergy between the security and intelligence agencies.
"This incident will serve as a lesson for all the agencies to cooperate and share intelligence," the source quipped.
The ownership of the cash haul has continued to generate mix reactions among Nigerians, with many asking pertinent questions - if the money was truly meant for covert operations as the NIA claimed, why has it not been spent in two years? Was there any need for it, considering how long it has stayed unspent?
The EFCC has in the past weeks recovered about N16 billion has been in Lagos.
About N12,360,814,000 and N4billion were traced to private accounts.