The union representing the athletes claims that a large chunk of the amount owed has not been paid by the Andalusian club.
The Rosaleda outfit was purchased by a member of the Qatari royal family in 2010 and has since purchased talented players like Martin Demichelis, Santi Cazorla and Joaquin.
However, Rubiales has claimed that Malaga has not been fulfilling its 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 percent 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 playoff round.
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