The deal was ratified yesterday and means that Japan and the EU can trade freely with each other.
This also means that 99% of all tariffs are removed making trade a lot easier.
The news has been welcomed by the ICMSA who say it offers serious potential for Businesses.
The say it is now up to the Agri-food sector to make the most of this opportunity according to ICMSA president John Comer.
He says it is positive to see an actual deal which is of benefit to the EU Agri-food sector, unlike negative agreements in place such as the much publicised Mercosur.
Mr, Comer added that the Free trade agreement now in place is a win-win all round and says it is now important to maximise its potential to the fullest.
He says this can be done by delivering stronger returns to primary producers.
Japan is already one of the world’s leading food importers, with an estimated $60billion of imports made in the year 2013 alone.
The country is now the worlds 4th largest food importer and the largest meat importer in the world.
Mr. Comer said Japan need to import up to 60% of its food every year to meet high demands. This he says creates a new opportunity for Irish food producers to explore, especially in beef and dairy produce.
He says it is now vital that the Department and Bord Bia play a huge role in helping maximise this new markets potential.
Mr. Comer spoke in terms of Brexit and this new deal, saying that it helps Ireland diversify its markets for life after Brexit, and said the European commission must be acknowledged for their hard work on the deal.
He concluded by calling on the Agri-food sector to grasp this opportunity with both hands.