The mining magnate, whose club's A-League license was stripped by the FFA on Wednesday, said he had registered a body named "Football Australia" to act as an independent watchdog on the association's governance.
"Football Australia will look at things like the corporate governance, the rights of fans, the rights of players, payments to clubs, payment to FFA, royalties, issues of that nature," Palmer said in a rambling media conference in Brisbane.
"We'll look at specific issues such as why was A$46 million ($49.70 million) spent [and] we only got one vote in the World Cup," he said, referring to Australia's failed bid for the 2022 tournament, which was awarded to Qatar.
"Why do the top five executives in the FFA get paid A$5 million a year while players, some of them get only A$50,000 a year?"
Gold Coast United, bottom of the 10-team league with four rounds of the regular season remaining, had been involved in a battle of wills with the FFA after putting the words "freedom of speech" on their shirts last weekend.
The row was precipitated by Palmer's comments to a newspaper last month in which said he did not like football, which he thought a "hopeless" game, and preferred rugby league.
The FFA lost patience with Palmer on Wednesday and stripped the club of its licence, saying the club had brought the league, its governing body and the game into disrepute.
Gold Coast United responded by saying the FFA had over-reacted and that the shirts statement referred to a separate dispute involving Palmer's group of companies against club sponsors Hyatt.
It was also aimed at highlighting the plight of refugees, according to club chief executive Clive Mensink.
The dispute, which pits billionaire tycoon Palmer against the financial and political clout of FFA chief Frank Lowy, Australia's richest man, has embarrassed the governing body and is likely to play out in the courts.
"We believe that [decision] breached natural justice, so tomorrow in the supreme court of Queensland we'll be seeking an injunction which foreshadows a legal action which the club will be taking against the FFA and against its members," Palmer said.
The FFA said in a statement later on Thursday that it was expecting the action and was ready for it.
"Once again an array of unsubstantiated claims and wild commentary have been made by Clive Palmer," FFA chief executive Ben Buckley said, referring to the media conference.
"The comments serve no purpose in any way to advance football in Australia."
Former A-League boss Archie Fraser, appointed CEO of "Football Australia", said he wanted the FFA to embrace the organisation and denied it was set up with the eventual aim of empowering club owners to launch a breakaway league.
"Clearly when you get senior identities who own the clubs complaining about a whole range of things, they need a voice and hopefully I'm a conduit to deliver that," he
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