The EFCC also impounded the international passport of the suspended National Coordinator of the National Social Investment Programme Agency (NSIPA) Halima Shehu.
The trio are being interrogated over allegations of financial crime levelled against them.
The passport seizure was part of the conditions for granting them administrative bail.
The travel papers are to be with the commission pending the conclusion of the investigation.
EFCC source said: “We have asked all those under interrogation to submit their travelling documents. We have seized the passports of Betta, Sadiya, Halima and others.
“For Betta, who was grilled from 11 am till 6 pm, she was the last to be granted bail yesterday.
“We demanded their passports to restrict their movement, to enable them to be available for interrogation. They are all cooperating with us.”
Sources said the three managing directors of banks were quizzed over their suspected conspiracy.
The banks were accused of refusal to raise “red flags” and gross involvement in suspicious transactions.
The banks were alleged to have violated the Anti-Money Laundering Act (Amendment) 2023, especially Sections 5, 10, and 16(b).