Hughes is said to have become unsettled due to the problems concerning owner Thaksin Shinawatra.
The new City board is also thought to have tried to sell Stephen Ireland and Vedran Coruka above Hughes' head, which he understandably feels has undermined his position.
Hughes is now the favourite to become the first Premier League manager to either be sacked or resign this season, but the ex-Blackburn boss has reiterated his commitment to the City cause.
"There have been a lot of rumours flying around but I am not going anywhere, and I don't anticipate going anywhere," he said. "There is a job to do here and I am looking forward to it.
"There is speculation around the club and that has been prevalent since I joined, but from my own point of view, I am very focussed on what I am about and what I aim to achieve here and that means success on the pitch.
"Nothing whatsoever has changed in that respect and the football operation hasn't changed since I signed for the club. Nor has my relationship with Garry Cook and his team. We get on really well and continue to speak on a daily basis.
"I am the guy that makes the decisions in relation to the football, and they make the decisions in relation to the running of the club."
I don't see how the situation with Thaksin would have affected Hughes. We've been aware of those problems since he took over the club.
The situation with the board is different, though. It does seem that they have tried to sell Corluka and Ireland without his knowledge, and this from a group of individuals that are supposed to be his team. They all came aboard this summer so you'd expect them to all be singing from the same hymn sheet.
Hughes has confronted the City board and left no doubt as to how he feels about it. His latest comments may allay fears he is about to chuck it in, but if there is any more interfering from the City board, he'll be on his bike.
Hughes is a proud man and he just won't stand for it. That's how they operated at Blackburn, they left him to it, and just look at what he managed to achieve.
The board needs to get its act together before we drive away another great manager.