Negotiations between the two countries were concluded in April last year, with tariffs to be cut on exports for fresh, preserved and prepared beef from Australia.
Howard Smith, president of the CCA, said the finalisation of the deal put Australia ahead of competitors in securing better market access for its beef.
"Japan continues to be an integral market for the Australian beef industry and the Cattle Council sees opportunities to grow Japanese demand for Australian beef through the implementation of JAEPA," said Smith.
"The flow-through benefits of reducing burden from the supply chain, through the implementation of JAEPA, should provide an opportunity for greater farmgate prices, with modelling suggesting a boost in the annual gross value of Australian beef production by up to 7%."
He added that the implementation of JAEPA was "monumental", because it paved the way for greater trade reform with Japan via the Trans-Pacific Partnership and Regional Comprehensive Economic Partnership negotiations.
As part of the agreement, the tariff on fresh beef will be cut to 23.5% over a five-year period, while the tariff on frozen beef will be halved from 38.5% to 19.5%.