Manfred Bøtsch, director at the FAO, pointed out that "certification will help protect the origin, quality, and tradition of Switzerland's Emmenthal cheese", but other countries which produce the cheese claim the move is just a ploy to bolster flagging export sales.
Over the past two decades, Emmenthal exports have dropped by nearly a third and nearly half of all producers of the famous cheese have gone out of business.
But Emmenthal is still a prestigious name for the Swiss cheese industry, particularly on an international platform, accounting for more than half of Swiss cheese exports. Around 85 per cent of the 32,000 tonnes of Emmenthal cheese produced in Switzerland in 2003 were exported.
The Swiss FAO rejected 64 appeals against the geographical protection proposal, with objections received from France, Denmark and Austria - all of which have 30 days to appeal before the decision passes into law.
The Danish Dairy Council estimates production of Emmenthal at around 9,000 tonnes a year, of which 90 per cent are exported to principal markets, France and the US. Clearly, any attempt to enforce the Swiss PDO would cast a shadow over any future export activity.
The German Dairy Association reacted angrily to the Swiss move, making reference to a 1951 trade agreement, which states that all European producers of Emmenthal reserve the right to use the 'Emmenthal' name.
The European Commission was also quick to denounce the decision, throwing the validity of the ruling into question. EU officials claim the Emmenthal name has become a "generic expression" for describing the famous cheese, and is not just a label unique to Switzerland. For example, the cheese has been manufactured in Germany since 1820.
The FAO based its decision on three separate surveys undertaken by Swiss agricultural officials, which showed the Swiss closely associate the cheese with a specific part of the country, thus qualifying the brand as a PDO.
Obtaining the PDO status is by no means an easy task - there are a number of stringent conditions that specify exactly how the cheese is to be manufactured, such as using untreated milk which is no more than 24 hours old, and leaving the cheese to mature for four months before it can be sold.
Most of the 270 cheese producers who will benefit from the label are based in the Emmenthal region near the Swiss capital Bern.
Despite the numbers of obstacles Emmenthal producers have to overcome in order to receive the unique status, Guido Nydeggaer, of the Association of Emmenthal Cheese Producers, still believes that the standard will be beneficial to the industry, should it be introduced. "This will ensure good quality and restrict the number of producers," he said.
At present, the only PDO labels recognised by both the EU and Switzerland are limited to a handful of wines and spirits, although dialogue between both parties is still ongoing.
The FAO ruling will also lend Swiss-based producers of the cheese a considerable marketing advantage, gifting Emmenthal an added seal of approval in lucrative German and Italian export markets (Italy is the biggest importer of Swiss Emmenthal with 11,000 tonnes in 2003).
Despite the EU's opposition to the Swiss decision, it has disturbing echoes with one of the Commission's own recent rulings. In October 2002 the EU took formal steps to prevent feta cheese being produced in countries outside Greece, granting geographical protection to the cheese following years of lobbying by Athens despite the fact that more feta is currently made in countries such as France and Denmark - whose appeal of the 2002 decision is ongoing.
It is also not the first time the Swiss government has made a controversial attempt to secure a PDO certification for cheese - back in November 2003 a similar argument broke out over the use of the 'Raclette du Valais' name, which it ruled could only be linked to cheese producers in the Valais region.
This issue, however, did not attract as much widespread international criticism, as most producers of raclette cheese are other Swiss companies rather than international producers.