The former AC Milan and Inter midfielder dramatically left the field Sunday while playing for Pescara at Cagliari after he angrily confronted Cagliari fans, claiming to have been racially abused before being booked.
While leaving the pitch in frustration and murmuring "Basta ! (Enough)", Muntari went to address more supporters, showing them his arm and shouting: "this is my colour, this is my colour."
Muntari, 32, could now face disciplinary measures after deciding to leave the field seconds before full-time – a decision that earned him a second yellow card, and then a red, from referee Daniele Minelli.
"FIFPro believes Muntari's yellow card should be rescinded," the Dutch-based union said in a statement.
"Muntari was well within his rights to approach referee Daniele Minelli, as the first point of reference, to make his grievances known and seek a solution," it said from its headquarters outside Amsterdam.
FIFPro urged Italian football authorities to "hear Muntari's version of events, investigate why the situation was mismanaged, and take firm action to ensure this never happens again."
"No player should ever feel the need to take matters into his own hands, as Muntari clearly felt obliged to do, by abandoning the match or taking spectators to task for inappropriate behaviour," it said.
Muntari was at AC Milan when former teammate Kevin Prince Boateng angrily walked off the pitch while being targeted with racist abuse during a friendly with lower league side Pro Patria in January 2013.
It prompted a wave of support on social media, although football's ruling body FIFA, while applauding Boateng's principles, said it did not condone his decision to walk off.