The Chilean took charge of the Qatari-owned outfit in November 2010, and guided them to Champions League football via a fourth-placed La Liga finish last season.
The club spent big in signing the likes of Santi Cazorla, Jeremy Toulalan and Ruud van Nistelrooy, but have since run into financial difficulties.
Goal.com exclusively revealed that Villarreal had reported the club to Uefa over outstanding payments from the transfer of Cazorla.
And now a number of players, including the Spain international, are set to leave La Rosaleda, and it is understood that Pellegrini is also weighing up his options.
The 58-year-old was due to meet Moayad Shatat, the general manager of the club, on Thursday, but the Qatari did not return to Spain on time.
They are now set to meet on Friday, and there is significant doubt that the club can afford to pay the coach's €3.3 million annual salary.
Prior to taking charge at Malaga, Pellegrini coached Villarreal, Real Madrid, and a host of South American teams, including River Plate, Universidad Catolica and Universidad de Chile.
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