City paid out 12.87 million pounds on such fees from October 2008 to September this year -- the biggest outlay ahead of Chelsea's 9.56 million.
However, Hughes told reporters on Tuesday that City were always likely to top the list because they have conducted more transfer business than their rivals and his club's use of agents was proportional to their buying and selling of players.
"If you do a lot of deals as we've done - something like 35 in and out over the period the figures relate to - then, given that amount of expenditure and turnover of players, you'd expect to see that high figure in terms of agents' fees," he said.
City are the world's richest club after being taken over last year by Arab billionaire Sheikh Mansour bin Zayed Al Nahyan, whose money has helped purchase internationals such as Robinho, Carlos Tevez, Gareth Barry and Emmanuel Adebayor.
City's spending on agents was revealed in figures released by the league on Monday and has put the spotlight back on the club's transfer dealings while raising the question of whether that amount of money should be leaving the professional game.
But Hughes added: "You have to base every negotiation and deal on its merits. In some cases you feel the agent has done a really good job, and in others he's getting money for nothing.
"There's a role that has to be met, and agents fill that role at the moment and they get recompensed for that."
