Officials from the Office of the Director of Corporate Enforcement (ODCE) have visited FAI headquarters as part of the investigation into the footballing body, the Herald has learned.
Sources said a number of FAI officials were interviewed when officers from the State's corporate watchdog called to the HQ at Abbotstown in west Dublin.
Last night, sources said the investigation was at a "very early stage" and it may take years to be completed.
It is understood the ODCE has requested a large amount of financial documentation from the FAI.
Sport Ireland previously said it understood the engagement between the FAI and ODCE was "substantial".
Under the Companies Act, if a statement given to auditors is false, directors who knew it was false or failed to take reasonable steps to prevent the report being approved can be fined up to €50,000 or jailed for a term of up to five years.
Earlier this week, Deloitte, the FAI's auditors, filed a notice with the Companies Registration Office stating proper accounting records have not been kept by the FAI.
Deloitte believes the FAI is contravening the Companies Act in relation to the obligations and requirements to keep adequate accounting records.
It was previously revealed that the ODCE has received a detailed protected disclosure outlining a number of new concerns about governance at the FAI.
Yesterday, the chief executive of Sport Ireland, John Treacy, confirmed John Delaney is "not a part of the FAI any more", after he stood aside from his new role of executive vice-president pending an investigation.
"John Delaney has voluntarily stepped aside," Mr Treacy said.
"I can't really comment on that because that is a contractual piece with the FAI, but from what I gather, John Delaney isn't part of the FAI any more.
"He is on gardening leave, or whatever the description is. We have to park that and get on with our business."
Mr Treacy would not comment on whether he envisaged the permanent departure of Mr Delaney.
Meanwhile, plans to create a governing body at the FAI are expected to be delivered in July.
Aidan Horan, a director of the Institute of Public Administration, will head the new governance review group at the FAI.
Mr Treacy said he is confident the football association's new board will deliver the necessary culture change.
"They will be laying the framework for what the FAI is going to look like in the future in terms of corporate governance," he said.Lesson
"What's really important is that we have the right type of skills required for the board.
"The board of the FAI must lead the organisation and not the chief executive.
"That's a lesson that everyone has learned.
"You need independent people. From my experience dealing with a lot of governing bodies of sport, I know they add huge value.
"You need to have people that know the sport, but you need people of independent mind that can make the right decisions for the right reasons."
The Sport Ireland boss was speaking yesterday at the publication of the Sport Ireland Anti-Doping review for 2018.