PFA Scotland say Dunfermline's players have made an official complaint to the Scottish Football League over partial payment of wages.
The Pars squad received 20% of their salaries on Thursday but BBC Scotland has learned players have now been paid half of what they are due.
Manager Jim Jefferies held a meeting with the playing staff on Friday.
The team are expected to fulfil Saturday's First Division fixture against Partick Thistle.
However, players are still seeking assurances regarding the future of the club from the club's major shareholder Gavin Masterton.