Magilton is alleged to have been involved in a heated argument with midfielder Akos Buzsaky after the 3-1 defeat at Vicarage Road on Monday night but he has said in a statement that he has done no wrong.
"While passions can run high in football, especially after a poor performance, I categorically deny any allegation of wrong-doing following Monday's fixture," Magilton's statement read.
"I understand that the club has initiated an internal investigation, with which I will co-operate fully.
"This is an unfortunate situation and I look forward to resuming my responsibilities shortly."