Santi Cazorla has already been sold, according to Malaga teammate Enzo Maresca as Arsenal emerge as clear favourites to sign the Spanish playmaker.
Malaga announced last week they were undergoing a process of "internal restructuring" amid reports owner Sheikh Abdullah Bin Nassar Al-Thani, a member of the Qatar royal family, wanted to sell up after only two years.
The club said on Saturday Venezuela striker Salomon Rondon had not joined the rest of the squad on a pre-season tour to Italy because he was negotiating his exit, while Cazorla is widely expected to join English Premier League side Arsenal.
With his expensively assembled team crumbling around him, Pellegrini may also jump ship but Maresca told a news conference Cazorla was a key part of the Malaga project as they prepare to take part in the Champions League for the first time.
"He (Pellegrini) is fundamental for us, just as Cazorla and Rondon were fundamental and who have had to be sold," added the Italian, who captained Malaga for Saturday's 2-0 friendly defeat to his former club Juventus in his native Salerno.
Forward Francisco Portillo said the club's performance against Italian champions Juventus had left them with "positive feelings" despite the uncertainty over Malaga's future.
"It's not an easy situation for us and I think we are showing that we can put ourselves above all these things," added the 22-year-old.