Antonis was sidelined from Sydney's 1-0 loss to Melbourne City on Friday with Arnold revealing the 21-year-old has been struggling with a knee injury since returning to the club after being part of the Socceroos' triumphant AFC Asian Cup squad in January.
Antonis was set to headline the Olyroos, who are to depart for Chinese Taipei on Sunday, to play in the qualifying tournament as they begin their road towards the 2016 Rio Games.
But Arnold has other ideas and says he'll speak with Football Federation Australia (FFA).
"His knee is not real great. He's had in injections and he's still in pain," the coach said. "I don't want him to go away with the Olympic team.
"I think if he can't play tonight then I don't see why we should let him go. It's his tendon. He came back from the Socceroos with it and we've been trying to manage him ... but last week it flared up again."
FFA rules state if a player is ruled out of national duty with injury they cannot play for their club while the national team is away.
Arnold will be without marquee striker Marc Janko for next week's crucial away clash with front-runner Wellington with the Austrian away on national duty.
