The Phoenix's match in Wellington on September 4 against Adelaide United clashes with New Zealand national team friendlies against Iraq and Jordan, meaning the All Whites will take a large number of players from the A-League club.
FFA decided not to postpone the fixture because it would cause too much disruption to the season but forgot to let the Phoenix know.
"If that's the case, then I'm very disappointed," Pignata said.
"But as far as I'm concerned I haven't officially been told anything by the FFA regarding that game.
"Until I get confirmation from [head of the A-League] Archie Fraser I can't comment, but it's disappointing the FFA have gone to the media without coming back to the club first."
Pignata added that it would be near impossible for Phoenix to field a competitive side on that date.
"I assume you can [bring players in temporarily]," Pignata added. "We won't have enough. I want to understand the reasoning here."