Ali Mansur, Ali Khadher and Ali Abbas are the three players named by Iraqi Football Association Assistant Secretary Tariq Ahmed as having gone AWOL from their team's hotel on Saturday night.
Australia defeated Iraq 2-0 in Gosford on Saturday night, with it suggested the visitors' flat performance was partly due to minds being focused elsewhere.
Ahmed said the loss of the players would harm Iraq's chances of qualifying for the Olympics.
"This will affect the morale of the other players because we need them badly for the next match," he said. "They could have left after they had done their duty in the next match. This shows disloyalty to their country."