Chairman David Sheepshanks says the Blues intend to appeal against the £10,000 fine imposed for their yellow card tally at Plymouth last Tuesday. The FA fines clubs for having more than six players booked in any one game.
Town were fined £5,000 for totalling six at Southend with the fine for the second offence against Plymouth costing a further £10,000.
Sheepshanks says Town are determined to fight their position: "I am not happy with the second fine, firstly because we are not keen to hand over £10,000 and secondly because it prejudices our reputation in the game.
"Jon Bickers, our video man, is to prepare a film of all the yellow cards at Plymouth and send it off to the authorities.
"I am not going to knock referees for the sake of it, but we have been the victims of some very debatable decisions.
"And I want it to be brought to the notice of the authorities. We swallowed the pill over the Southend fine, and we might have to this time. But we feel we have a case."
The Town management and those fans that travelled to Home Park for the game were critical of referee Kevin Friend's performance. Friend's previous Town match was last season's game at Crystal Palace in which he red-carded loanee Ricardo Fuller having disallowed what seemed a perfectly good goal.