The Qatari billionaire has called upon the RFEF to protect his side after they suffered a "moral and psychological" injustice against Borussia Dortmund
The Andalusians were knocked out of the competition after a late, offside strike from Borussia Dortmund's Felipe Santana, prompting the Qatari to claim that his side were the victims of institutional racism.
He later backtracked on his criticism but has now called on the Spanish football authorities to protect his side.
"Firstly I'm sorry for Spanish teams' losses in the Champions League," he wrote on his Twitter page.
"I hope to refer to my comments from the past. I mentioned that there is a catastrophe in Spanish football. My question to the Spanish Football Federation is: where is the justice and equality between club?
"We were wronged by Uefa. Where are you for this injustice against Malaga and the moral and psychological damage?"
Malaga face a hearing to determine whether they will be allowed to compete in the Champions League next season after being found to be in breach of Financial Fair Play regulations.