Former Australia goalkeeper Reilly, whose six years on the board ended in 2013 after fallout with chairman Lowy over the tactics employed by FFA in its failed bid to win hosting rights for the 2022 FIFA World Cup, is concerned the selection process for November's election is 'not as open as it should be'.
He also queried the conduct of deputy chairman Brian Schwartz, who he claims has been chaperoning Steve Lowy – co-chief executive of Westfield Corp – 'all around the country meeting stakeholders over the last three months' in what Reilly believes is a defacto election campaign.
Though FFA has recruited search firm Egon Zehnder to help find new directors, with a nominations committee led by long-time Lowy confidant Schwartz, Reilly has grave reservations over what he sees as Lowy's dynastic ambitions when he steps aside.
"The position should be thrown open to whoever wants to put their hat in the ring but the way it is being handed right now is not a particularly open process in my view," said Reilly.
"The FFA board has been Frank's board for 10 years – it's as simple as that. Can you continue with that? I am not so sure.
"If everybody believes that Steven is the right man for the job then great – I just feel it should be a totally open and transparent process.
"I know some good people who might put their hand up but won't with what's going on at the moment."
Reilly - instrumental in laying the groundwork for the ownership structures of both Melbourne Victory and the newly rebranded Melbourne City – added: "It's time for a total review of the last 10 years ... what was good, what was bad and what needs to be put in place to ensure the game goes forward in the best possible way."
When D-day arrives in November - Steven Lowy has until September to officially nominate as a candidate - the 10 A-League clubs each will have one vote, with a further nine votes belonging to the state federations.
While Lowy will leave a legacy that includes the launching of the A-League, the move of Australia into the Asian Football Confederation and the Socceroos qualifying for three consecutive FIFA World Cups, Reilly contends that Lowy's best work has been beyond the football arena.
"Nobody can point a finger at Frank's success - but his success has been in his business (the Westfield shopping mall empire)," he insisted. "He's been absolutely brilliant at that.
"I have had huge debates with him over football though ... I don't resile from that. The only thing I understand is the total truth and if it's not that I will have the debate.
"The fact is that A-League owners have lost $240 million between them in the 10 years of the competition and the FFA have set the agenda. That needs to be looked at.
"What would happen if that $240 million was in the bank for the game? People have come into the game and gone, good and not so good.
"There comes a time when people look for a return on their investment, as well as simply just being involved in the sport.
"We had 200,000 fans attending the tour games of Roma, Manchester City and Real Madrid in Melbourne last week ... they are fans of the game, so what are we doing to get out to them?
"They are looking for a way forward and want the game to succeed. We need to put people in place who can deliver on a long-term plan.
"I would like to see the club owners treated as great supporters of the game and given every opportunity to succeed.
"It's all very well the FFA setting the agenda but who will ensure the delivery of that agenda?"
Lowy's relationship with Reilly has been frosty at best for some time and soured further when Reilly lashed at the methodology of Australia's FIFA World Cup bid last month, with Lowy hitting back: "It's easy to speak now. You were there for six years; you thought you changed the world. In fact, you did nothing in those six years.
"I don't remember anything major, or even sub-major, that Jack Reilly made a comment to the board that was taken into consideration."
Asked whether his views carried any traction during his time on the board, Reilly replied: "Well, according to Frank I did nothing for six years, although, by the way, I received a letter of apology from him for those comments four days after he made them.
"Of course it's nonsense ... where is the game most successful? It's in Melbourne. Who created that? I did.
"I got the FFA to invest $500,000 in Victory when former chairman Geoff Lord couldn't raise any extra funds and we got a 50 per cent return on that investment in eight months. And a business plan was put in place which has put them where they are now.
"Then when Melbourne Heart was struggling a bit I organised for Manchester City to buy them."
