The appearance of senior FAI officials before an Oireachtas committee this week has been described as a "new low" for Irish football.
Former CEO John Delaney was among those who appeared and refused to answer questions about a €100,000 loan he gave the organisation in 2017.
The PFAI - which represents professional footballers - said: “We have watched the events of the last few weeks with dismay culminating with the appearance by FAI representatives at the Oireachtas yesterday.”
“While many of the public were shocked by the inability of those attendees from the FAI and in particular the blatant stonewalling by the former CEO, unfortunately for us as players and for our representatives this is the standard response that we have become accustomed to over the last few years.”
“It is clear that the finances of the FAI need to be forensically examined and the governance of the association completely overhauled,” it said.
“Deputy Ruth Coppinger said yesterday that the hearing was 'like Hamlet without the Prince.' To continue the analogy, something is rotten in the state of the FAI.”
Legal advisor to the PFAI, Stuart Gilhooley, said significant reform is needed.
Mr Gilhooley said: "The buck stops with the FAI. They are the people who run the league and they have been running the league now for quite some time. It's definitely a fresh start, fresh blood that is required."
On Newstalk’s Off the Ball last night, former Irish international manager and player John Giles said the saga has been "one of the worst weeks for Irish football."
"I've never known a situation like this where the soccer community was in the position that we were in," he said.
Asked whether the entire FAI board should resign, he said: “it is something to be considered...(although) it sounds a bit drastic initially."
"I think a lot of thought should go into where it goes and where it goes from here. But that certainly would be an option along the way.
"There are big decisions to be made, there's no doubt about that. In my opinion anyway, it was a bad time for Irish football."