The governing body is currently conducting an independent inquiry into Craig Whyte's controversial takeover of the crisis-hit Ibrox club.
However, Regan has confirmed other issues have arisen during the course of the far-reaching investigation which will also be looked at in greater detail.
It has been speculated that Gers players had two contracts with the Glasgow club when EBTs were in use between 2001 and 2009.
And last week ex-Rangers director Hugh Adam claimed that specialist payments were being made to playing personnel as far back as the mid-1990s. Under the SFA's articles of association, clubs are only allowed to give players one contract of employment.
Regan admitted on Friday that the allegations made by Adam, who was ousted from the club board by former owner Sir David Murray, would be looked at. And he outlined the range of punishments available to the organisation if Rangers are found to have breached their strict guidelines.
He said: "If you look at our articles of association, it shows a range of powers that the judicial panel has.
"What will happen is that the matter will go to the Scottish FA main board and will then pass through to the judicial panel.
"There's a whole range of things from suspension to termination of membership at the extreme end to fines and ejection from the Scottish Cup or other such penalties the panel deem appropriate.
"It (Hugh Adam's claim) is one director's take on things, but, as a board, we have to examine it."
Regan added: "The inquiry covers primarily the Craig Whyte era, but in digging into facts it has take us into other areas.
"It's thrown up matters which are of interest to the committee. I'm there representing the board. We've got into the meat of what has been going on at Rangers and now the inquiry has gone in different directions.
"The inquiry isn't judge and jury. The process is one of investigation and presenting the facts.
"The board will consider the facts and if the board feels the facts are compelling they will pass that to the compliance officer and it will go through the normal disciplinary process."
Regan refused to dismiss the possibility of a separate inquiry being launched specifically into allegations of double contracts at Rangers in the future.
He remarked: "That will depend on the board's view of the facts and what information there is. The situation is changing daily and new information is emerging all the time.
"We've got our hands on certain pieces of information and we're exploring it and asking for further information. If it's the board's opinion that they want a fuller investigation then that will be an option."
Meanwhile, Regan has confirmed that SFA president Campbell Ogilvie, whose role at Rangers during the Murray era has come under scrutiny, will not be involved in any investigation into secret payments.
He saud: "I think it's pretty obvious that he (Ogilvie) is heavily conflicted. Campbell won't play any part in any meeting, discussion or conclusion on any activities surrounding Rangers."