The governing body and its chairman have stated their preference for a local to succeed Holger Osieck and take the team through to the World Cup and Asian Cup
The identity of Australia's next coach has been debated all week after Holger Osieck was sacked following disastrous 6-0 drubbings to Brazil and France.
High-profile candidates Guus Hiddink, Marcelo Bielsa and Zico have all been linked to the vacancy ahead of next year's FIFA World Cup in Brazil.
But calls for an Australian to lead the national team have grown louder by the day, with Ange Postecoglou [Melbourne Victory], Graham Arnold [Central Coast Mariners] and Tony Popovic [Western Sydney Wanderers] leading the way.
And Lowy has confirmed the FFA favour a local coach ahead of an overseas appointment, with a decision expected in the next fortnight.
"When we appointed Holger [Osieck] coach three years ago, I recall I said words to the effect 'I hope the next coach will be an Australian'," Lowy said on Tuesday.
"That was the plan and is still the plan.
"Our preference is clearly for an Australian coach.
"Three names are being talked about and it's not wrong that we have three possible Australian candidates.
"Hopefully we will come to terms with one of those three, and failing that we'll need to find somebody else from overseas."
Lowy and the FFA hierarchy are aware any potential decision could disrupt an A-League club so early into the new season, which has led to suggestions the chosen candidate could continue in a dual role for the rest of the domestic season.
"The dilemma we have is how to keep the balance because the season has just started and the clubs have worked very hard to set themselves up," Lowy said.
"So it's up to us to find a way to negotiate with whoever we pick and see what can be done so as not to disrupt their plans.
"One club may be more reasonable than another and we need to be mindful of that, after all the A-League is doing extremely well.
"It will be a joint discussion, the club has to have a big say in what they are prepared to do."
Osieck's successor will be tasked with overhauling an ageing squad, after the German failed in his job description to introduce and develop younger players.
Though Lowy is adamant the FFA have learnt from their mistakes.
"I think we're wiser now than we were three years ago," he added.
"I would expect that we would talk to the coach and make up our mind whether he will fulfil the criteria that we put to him.
"But once we appoint him we can't tell him what to do.
"We want to have a credible performance at the World Cup and win the Asian Cup. That was our goal then and that is our goal now."