In a statement, the PFAI said the appearance of FAI board members before the Oireachtas Sport Committee this week was a "new low" for Irish football.
Former CEO John Delaney repeatedly refused to answer questions about a €100,000 loan he gave the organisation in 2017.
He also refused to answer questions on the FAIs finances or his former role as CEO.
The PFAI 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 warns that the League of Ireland has been the “poor relation” of Irish football for years – with priority given to the International team and grassroots football throughout Mr Delaney’s 14-year reign as CEO.
“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.”
PFAI chairman Gary Rogers said the FAIs Oireachtas performance was a “new low point for Irish football.”
“In a country where soccer remains the most popular sport, the lack of priority given to our own league is embarrassing,” said.
“The prize money available for winning the League is disgraceful; it has halved since 2007 and is disproportionate to what clubs pay for affiliation fees.
“There needs to be root and branch reform within the FAI.”
On Newstalk’s Off the Ball last night, former Irish international manager and player John Giles said the sage has made up "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.”
“It sounds a bit drastic initially," he said.
"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."
The committee heard that the FAI board was not informed of the loan the association received from Mr Delaney – despite the fact that previous press statements suggested it was fully aware of the situation at the time.
Mr Delaney said he only informed the board two years later – after receiving a media inquiry from The Sunday Times.
It remains unclear whether the payment was recorded in the FAI accounts; however, the association admitted that it breached State funding rules by not informing Sport Ireland of the loan.
Sport Ireland has since announced its decision to temporarily 'suspend and withhold' future funding to the FAI until the association can prove it is compliant the rules.
The State body approves around €2.9m in grant funding for the FAI every year.
