Plans to overhaul the contentious profit and sustainability rules (PSR) were recently postponed due to legal disputes.
The proposed squad cost ratio (SCR) system was set for 2025-26 but will now undergo further testing before implementation.
"There's no civil war - that would not be the way that I would put it," said Masters, who was speaking at the Financial Times Business of Football Summit.
"Alignment among Premier League clubs has never been easy. Maybe it's a little bit more difficult at the moment.
"But to change to a new system, particularly with what's at stake, is a big decision. If clubs need more time to do it, then that's OK. We will carry on that path.
"We've agreed in all probability on PSR in 2025-26 and then we'll look again during the course of that season at whether we'll make the move to SCR."