Paphitis said: "I find the whole thing staggering. The charges are completely ridiculous. There has never been a discussion after the game suggesting there was any racist abuse. It is completely out of the blue and I find it personally insulting. Racism is too important a subject to pointscore on.
"The FA seems like a rudderless ship at the moment looking for publicity. We will respond and invite the FA for discussions.
"Maybe they will leave their palace at Soho Square to come and talk to us about the evidence they have to make these charges."
The FA arrived at the charges after examining video evidence and reports from the game and full details should be with both clubs today.
Millwall will review them before deciding on how they will respond but Paphitis indicated they would refute missile throwing accusations.
They allegedly failed to stop their fans throwing coins and lighters but Paphitis said: "We have got details of seven incidents of coin and lighter throwing during the game from the police. All were identified as coming from the Liverpool end."
Liverpool spokesman Ian Cotton said: "We are disappointed to have been charged by the FA and will consider our response in due course."
