A previous rule allowing Phoenix to sign replacements has been changed, leaving Merrick to rely on the back end of his wafer-thin squad.
It's understood that Phoenix submitted a request to FFA to have the City clash moved to the split round in March.
Merrick confirmed that he was set to lose players for the opening week of the season.
"We'll be compromised for the first two games of the season, which are so important for any club," Merrick said.
"We've put together a good squad but this works against us in trying to produce our best results.
"It will also cost the Phoenix fans the chance to see Tim Cahill in round one."
Phoenix have recruited strongly after a turbulent year where the FFA questioned their A-League future before granting the New Zealand side a 10-year license extension.
Barbarouses and Gui Finkler were signed from Victory while highly-rated Italian defender Marco Rossi has also joined.