Commenting on the achievements of 2012 and the challenges that lie ahead in 2013, Mr McNaughton hoped that the 'unfinished business' of CAP reform might yet produce measures to boost stock numbers.
"The downward drift in cattle and sheep numbers is a massive negative for Scotland's meat industry, adding to the sector's unit costs and depriving the whole country of valuable jobs and income at a time when just about every other industry would love to have our market opportunities, both at home and abroad," he said.
"We have great natural resources, served by a top class production, processing and marketing chain. Unfortunately, the CAP mistakes of 2003, which we warned about at the time, have resulted in a steady erosion of livestock supplies, leading to missed sales opportunities, company closures and a substantial amount of lost business for Scotland plc.
"We've been banging away at this issue all year, urging Government leaders in Edinburgh, London and Brussels to make sure the current CAP reform includes special measures for Scottish livestock producers.
"We're not asking for financial aid to keep livestock producers and meat companies in business, however, or seeking support for an industry which is failing or unprofitable," he stressed.
"We're merely asking for Scottish, UK and EU politicians to invest in a sector of the economy which has the capacity to repay such confidence many times over in terms of reduced spending on imported meat, increased earnings from meat exports and a serious commitment to long-term meat sector jobs.
"We must also never under-estimate the contribution which livestock farming makes to environmental betterment in the uplands; it's the existence of sufficient cattle and sheep on the hills which drives the kind of environment which makes Scotland such an attractive place," he added.
"These are powerful reasons to justify the increased support for calf and lamb production we are advocating. Furthermore, those who say 'let market forces decide' are being naive if they think that will result in anything other than the exporting of Scotland's beef and lamb business to India, China, Brazil and elsewhere, rapidly followed by rising costs for buying back the end products we could, and should, be producing at home.
"We will keep seeking to drive this message home in 2013. Frankly, the future of Scotland's meat and livestock chain depends on it."