Man City chairman frustrated by financial storm over treble triumph
Pep Guardiola's team won a historic treble of the Champions League, Premier League and FA Cup last season - becoming just the second English side to manage the feat.
City were charged in February with 115 alleged breaches of the Premier League's financial fair play regulations dating back to 2009 and accused of not cooperating in an investigation.
Guardiola last month said he does not want a cloud hanging over his side's achievements and hopes for a resolution as soon as possible.
Khaldoon, speaking to in-house club media, said he could not comment in detail on the charges for legal reasons but would have a "conversation" when the process was complete.
"I'll give you my very blunt views, I promise you that," he said. "I have very strong views on that, but I am going to be unfortunately very restrained today.
"It's very frustrating because it takes so much from the great work that's happening at this club and it's happening not just on the football pitch. The football pitch - what these players have achieved this year, the treble, is incredible."
Khaldoon said City, who have won five of the past six Premier League titles, were "very well run".
"Today, the value of this group is over $6 billion," he said. "We've created so much value - we've brought in world-class investors. Why? Because we have a commercial machine here that is one of the best in the world."
Khaldoon believes City are the top football brand globally.
"We can go on for half an hour right now with me just giving you data in terms of net spend over the last season, net spend over the last three years, over the last five years, over the last 10 years," he said.
"Look at every single one of them and just look at these as the facts and compare us to our competition and then people will throw at us 'you're the biggest spenders', 'you have the biggest squad'.
"I wish people can just pause and ask the question and get the facts and then comment."