Former FAI boss John Delaney raised fears about the impact of Brexit on Irish football shortly before details emerged of his loan to the association.
His concerns included a loss in funding he said has already occurred.
In a letter to Sports Minister Shane Ross, Mr Delaney also warned of a threat to Irish teenagers being able to play for British clubs and asked the Government to consider the matter in Brexit negotiations.
The correspondence was sent in February, a month before it emerged Mr Delaney had made a controversial €100,000 loan to the association in 2017.
Mr Delaney has insisted he acted in the best interests of the game when he extended the interest-free loan.
However, the revelations sparked intense scrutiny of the FAI's finances and governance.Disadvantaged
He wrote to Mr Ross on February 13, saying: "The association has already lost funding for a very important initiative 'More than a Club'."
That scheme aims to assist clubs in the development of social enterprise to help disadvantaged communities.
Mr Delaney said it was being run in Bohemian FC in Dublin, as well as at Cork City FC, and it was a joint initiative with Wales which was funded by the EU.
"As Wales are now leaving the EU, funding for this valuable project has been withdrawn," he wrote.
He added that this puts the project and four jobs it has created "at risk" unless alternative funding can be found.
Last night, the Department of Transport, Tourism and Sport said no offer of funding was made by ministers in response to the letter.
The FAI did not answer a question on how much funding had been provided for the initiative by the EU.
A spokesman said the 'More Than A Club' project is due to come to an end this summer.
"A small amount of funding has been secured to extend the programme for a short period of time and all involved are aware of this," the spokesman said.
The statement did not say where the funding came from for the short extension.
Bohemian FC said the funding for the 'More Than A Club' initiative was given to the FAI who employed staff to work on behalf of the northside team.
A statement said the funding ends on May 31 and added: "It was always an 18-month project under the European Regional Development Fund's Ireland-Wales Programme, but it was hoped that additional funding might be found to continue it."
Two full-time and one part-time staff members were employed and are still working on the project. Bohs said the terms and conditions were between the FAI and the staff.
Mr Delaney also expressed concern about the ability of young Irish players to join professional clubs in the UK at the age of 16.
"Whilst the SSE Airtricity League clubs have now developed an academy system in Ireland with a clear elite pathway to play professional football, a number of our promising players continue to move to the UK at the age of 16 to join professional clubs in the UK," he wrote.Conditions
He said there is an exception in Fifa regulations that allows players within the EU or EEA (European Economic Area) to transfer to clubs within that territory, subject to a number of conditions, including guarantees about education.
He said that given the uncertainty surrounding Brexit it is unclear what effect it would have on players who are currently in the UK and who have not yet reached their 18th birthday.
According to Mr Delaney, "facilitating our top elite players to play full-time football at the age of 16 has a significant impact on their sporting development and ultimately benefits our national team".
"We would ask the Irish Government to take this issue into consideration when negotiating on Brexit as if the UK remain in the EEA this will allow the Fifa exception rule to still apply."
John Giles yesterday said the right to do for Mr Delaney was to resign.
Questions surrounding how funds linked to the John Giles Foundation are operated were raised in a protected disclosure to the Office of the Director of Corporate Enforcement.
But speaking on Newstalk radi Mr Giles said he was confident money that came into the trust went out in grants.
"I think that there is such an amount of criticism now, and things have got to such a stage where the right thing to do would be to resign," he said of Mr Delaney.