Recent rumours had claimed that the pair exchanged a difference of opinions before the club's 0-0 draw with Fulham a fortnight ago - a match that Holt missed with a reported back injury.
However, Hughton has insisted that any talks of a disagreement "are way off the mark".
"[It is] absolutely not true and I am very, very surprised to hear that," Hughton told reporters. "Grant has been an integral part of what we've done - not only this season but the last three seasons.
"He's got a great record and that is why he is the club captain. Any suggestions are way off the mark and I'm not quite sure where they came from."
Holt joined the Canaries from Shrewsbury Town in July 2009.