City are facing 115 Premier League charges for breaching numerous financial regulations.
This season they became the second English team to achieve the Treble of Premier League, Champions League and FA Cup after Manchester United in 1999.
“What these players have achieved this year is incredible,” Khaldoon said.
“I hope people focus and judge them for their football and what they’re achieving on the pitch and what they’re achieving in every competition they’re in. That’s the reality.”
City have been referred to an independent commission for more than 100 alleged rule breaches between 2009 and 2018, and manager Pep Guardiola has said he would like matters dealt with immediately.
Speaking in an end-of-year in-house interview, Khaldoon said:
“It’s very frustrating because it takes so much from the great work that’s happening at this club.
“The club as a whole is well run – very well run.
“I can’t talk about them (the charges) unfortunately for legal reasons. These are proceedings that take whatever time they take and when we’re done, I’ll give you my very blunt views. I have very strong views on that, but I am going to be unfortunately very restrained today.”
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