The official is currently being investigated by authorities after Chelsea claimed he used "inappropriate language" towards John Obi Mikel in the Blues' league defeat to Manchester United last week.
Clattenburg is co-operating fully in the proceedings that have also attracted the attentions of the Metroploitan Police.
Hughes saw one of his players, Anton Ferdinand, embroiled in a long-running legal saga over John Terry's racial abuse of the defender and believes that a similar situation, that saw Terry play on for a year before he was finally punished, must be avoided.
"It's difficult when the authorities get involved, as we found with Anton and John. It ended up going on far too long," Hughes told The Sun.
"The authorities seem to be involved with Mark Clattenburg too and you don't want it to drag on."