The union representing the athletes claims that a large chunk of the amount owing has not been paid by the Andalusian club
The Rosaleda outfit were purchased by a member of the Qatari royal family in 2010 and have since purchased talents players like Martin Demichelis, Santi Cazorla and Joaquin.
However, Rubiales has claimed that Malaga have not been fulfilling their contractual obligations towards the players and dismissed the notion that the AFE is against foreign ownership of Spanish clubs.
"On June 31, Malaga's players were owed 35 to 40 per cent of their wages," he told eldesmarquemalaga.com. "A significant sum of cash is owed.
"There have been some complicated situations and we cannot avoid it. The true Malaga fan wants the club to continue to compete with the best conditions.
"There is no one special here, whether they are from Qatar, Japan, Madrid or Huelva. There is a regulation, which I am sure can be improved, because in football things must be done seriously."
The AFE president then revealed that Malaga's players have until the end of Monday to report the situation to the league, but refused to say whether anyone will do it.
Malaga finished fourth in La Liga in 2011-12 and will play in the Champions League play-off round.