Chelsea and England captain Terry has been charged with racially abusing QPR defender Anton Ferdinand but will not stand trial until July 9, meaning he will be able to play at this summer's Euro 2012 finals.
Hughes is disappointed the matter will not be settled for almost six months and also claims it will disrupt his club's pre-season preparations.
"They've made a decision that impacts on one of my players, they've given a date which is slap bang in the middle of pre-season,'' Hughes said.
"I don't know how they've come up with the date, whether they have had discussions with the FA and made sure it doesn't impact on the Euros.
"If John goes to the Euros it probably impacts on his holidays. But it's not in Anton's down time.
"It seems to have been dragging on forever. Certainly from my point of view and Anton's, we'd have preferred it to have been done and dusted by now.
"We weren't involved in any discussions, otherwise we would have put our point over that there could be a little bit of an issue from our point of view.''
Terry, 31, is accused of a racially-aggravated public order offence over video footage which appears to show him shouting an offensive comment at Ferdinand during a Premier League match in October.
The Chelsea defender, who faces a maximum fine of £2,500 if convicted, has repeatedly denied making the alleged slur during the game at Loftus Road.