Fowler A-League future in doubt
Fowler refused to play in Saturday's 1-1 draw against Brisbane Roar, after coach Ian Ferguson changed his playing formation and moved Fowler to the bench.
The 34-year-old instead sat in the stand in street clothes.
Fury chairman Don Matheson said he would talk to Fowler, the highest-profile signing in the five years of the A-League, on Monday.
"They were unlucky not to take the game and, although Robbie has been fantastic for the club, we're not a one-man team," Matheson said.
"He's here to play football. He didn't play last night for reasons between him and the coach.
"Obviously I've been set up to speak to Robbie to sort out their differences.
"It didn't pan out the way I would like so I will probably intervene on that tomorrow and we'll move forward from there."
Fowler joined the Fury last year after finishing as the fourth highest scorer in England's Premier League with 161 goals.