The operator, which is one of Ireland's biggest international freight firms, has some 50 trucks and more than 350 trailers on its fleet, and was originally charged with technical offences relating to the unladen weight of the vehicle at the time it was taxed.
"The laws for commercial vehicle motor tax were written in a different era," insists Chris Smyth, commercial director of Perennial Freight, which is based in Wexford and has offices in the UK, France, Holland and Poland.
"The mixed nature of our business means that, on some occasions a tractor will have to pick up a trailer heavier than the one it was originally taxed with," he explains.
"If this happens, we could be prosecuted for an offence... We think this is unfair and unreasonable. We don't believe that the Oireachtas intended the law to be this way when they wrote it. That's why we have asked the Supreme Court to consider the fairness of these prosecutions against us."
FTAI's national council voted to financially back the court action because of its implications for the freight industry in Ireland as a whole.
"Ireland has the highest rates of commercial vehicle road tax in Europe," states Jon Goodaker, operations manager of Virginia International Logistics and chairman of the FTA Ireland National Council.
"The only way operators like Perennial Freight could be compliant with the law as it stands is for them to tax every single truck they have at €5,195 per year," he continues.
"This would make them even less competitive against UK and continental operators, and threaten employment in the company. The laws as they stand should be struck down."
Neil McDonnell, general manager of FTA Ireland, makes the point that this is a long-running issue for the freight industry in Ireland.
"We have pressed the Dáil and the Transport Minister on motor tax, to no avail," he explains.
"It is apparent that many international transporters are now registering their operations abroad to avoid the oppressive rates of taxation in this jurisdiction. This also means a loss of driver employment in Ireland."
McDonnell says the Commission on Taxation, set up by the Oireachtas, identified shortcomings in commercial motor tax and suggested remedies as long ago as 1984.
"There is no point in Dáil Eireann setting up high-powered commissions, and then ignoring their recommendations," he insists.
"Successive governments have done nothing to rectify the situation, leading to the ridiculous position today, where thousands of prosecutions have been made against otherwise law-abiding employers.
"We believe it's time the Supreme Court delivered a message to the legislators to get their house in order. 31 years of inaction on this issue is enough."