City have already had offers of £15million and £18million rejected by the Goodison Park club, who insist the player is not for sale.
Everton's firm line on the matter has also seen them reject a written transfer request from Lescott but Hughes today indicated he is not yet ready to give up.
"We have made offers and shown interest, obviously that is seen by virtue of the bids we have put in," said Hughes, who has already spent close to £100million in the summer transfer window.
"But they have been rejected and Everton are fully within their rights to do that, we respect that.
"We are still trying to speak to the people who will ultimately make the decision over whether or not the deal continues.
"Those conversations are still to take place but how long they will still be active is open to debate.
"It comes down to the club themselves and if they feel they don't want to do a deal in terms of the players they have they have a right to do that, and we respect that, irrespective of the player himself or how he feels."
If a deal for Lescott fails to materialise Hughes is likely to move on to other targets before the transfer deadline at the end of the month.
City have already signed one defender this summer in £16million man Kolo Toure from Arsenal but West Ham's Matthew Upson is another player to have been linked with Eastlands.
Hughes added: "We were looking to strengthen the defensive options we have got. We have done that in respect of Kolo, we are very pleased he is here.
"I have stated we would like further strengthening to take place but if not we go with what we have got."
City were involved in additional controversy this week over the withdrawal of striker Craig Bellamy from the Wales squad.
Bellamy did not report for his country's international against Montenegro last night due to a knee injury but the Football Association of Wales were not told in advance he would not be arriving.
Hughes admitted this was a mistake on the club's part and insisted there was nothing sinister in the withdrawal.
He said: "It was just a mis-communication. We haven't got a problem with players going away on international duty.
"We had 17 or 18 players away so it is not that we stand in the way of players.
"He had a reaction after a game and it was a case of trying to protect him not only for ourselves but for Wales, because they have still got qualifiers to come and I am sure he will be available for them.
"We apologised to the Welsh FA, it was down to us. We should have informed them."
Bellamy is now hoping to prove his fitness to feature in Saturday's Barclays Premier League opener at Blackburn.
Hughes said: "There is a difference between light training and full-blooded internationals.
"People were trying to make a little bit of mischief in that respect. We have protected him this week and he hasn't had a reaction since."
Former Rovers striker Roque Santa Cruz will miss the trip to Ewood Park through injury and there could also be a doubt over fellow new arrival Emmanuel Adebayor.
The £25million arrival from Arsenal suffered a minor groin injury on international duty for Togo in midweek.
Ex-Manchester United star Carlos Tevez should be fit after overcoming a heel injury aggravated by slipping in the shower.
Hughes said: "Carlos has had some good work this week and we are pleased. He hasn't had a reaction to his injury so he is looking in good shape."
Expectations at City have risen due to the club's lavish outlay on new players.
Having overcome conjecture over his own future throughout last season, Hughes is confident he can handle the pressure.
He said: "Everybody else was speculating about every aspect of Manchester City without being in full possession of the facts.
"I knew very early on what the situation was going to be and I was quite comfortable from an early point in the season, irrespective of what everyone else was saying.
"I've just been getting on with my job, that's what you do."
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