The Asian Cup-winning coach had initially refused to take sides in the battle and fumed at both parties after the row disrupted his preparations for Thursday's World Cup qualifier against Bangladesh and next Tuesday's fixture in Tajikistan.
But in a FFA statement issued on Wednesday, Postecoglou retracted his views.
"As a senior employee of Football Federation Australia I understand that my comments were inappropriate," the 50-year-old Greek-born coach said.
"I appreciate that I need to take sides on this issue. The commercial performance of the Socceroos brand directly affects the amount of investment in the match schedule, technical developments and sports science staff.
"In this case, the commercial boycotts imposed by Professional Footballers Australia (PFA) will directly affect commercial partners and will inevitably hurt the Socceroos programme.
"I made comments yesterday out of frustration. I acknowledge that the PFA initiated the regrettable situation that has distracted us in Perth. I understand that FFA was compelled to respond in order to explain its position to the game's stakeholders.
"I call on the PFA to undertake that no future Socceroo camp will be targeted in this way."
The tone was in stark contrast with Postecoglou's initial view of the impasse.
The strong-willed Australian said he was "not happy" the row had been played out in camp, and added he wanted to be talking instead "about selection, team tactics.
"If we think it's OK during the World Cup qualifiers to play out this scenario then I'm out of whack with everyone else because I think while the camp is on... lay down your guns and pick them up as soon as it's over, and go as hard as you want," he said.
"It's not good enough."
(Writing by Patrick Johnston in Singapore; Editing by John O'Brien)
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