The farmers' union says it will ultimately provide Australia with 'unfettered' access to UK food and drink markets through a deal that has 'yet to have any proper parliamentary scrutiny'.
It added that the process in agreeing the deal sets a 'dangerous precedent' for future trade deals, with the potential that the cumulative impact of all such deals on Scottish farmers and crofters will be 'substantial'.
NFU Scotland president Martin Kennedy said: 'As detail on the proposed terms of agreement around an Australian trade deal emerge, deep concerns will remain about its impact on Scotland's farmers, crofters and our wider food and drink sector.
'Under the proposed deal, there is to be a cap on tariff-free imports from Australia for 15 years. That is merely a slow journey to the Australians getting unfettered access to UK markets and with no guarantees that the promises of other safeguards will address the fact that very different production systems are permitted in Australia compared to here in the UK.
'The deal has not been afforded the appropriate level of scrutiny and consultation and has been agreed in advance of the promised statutory Trade and Agriculture Commission being established to scrutinise such deals.
'Parliamentarians must be given the opportunity to examine this deal, and any future deals, with the government carrying out a detailed impact assessment on what it may mean for the agriculture and food sectors.
'A free trade deal with Australia, and the way it has been agreed without proper industry consultation or scrutiny, sets a dangerous precedent for other free trade agreements, including those with other major farming and food producing nations such as New Zealand, Canada, Mexico and the United States.
'The cumulative impact of all such trade deals on extremely vulnerable sectors such as farming, food and drink could be hugely destructive.
'We are ambitious to identify and grasp opportunities to build our industry and wider economy and our reputation for world class produce.
'Trade deals could be an enabler of this, but it is going to require collaboration between UK Government and the industry; collaboration which does not exist at present.'
A UK Government spokesperson said: 'This deal delivers for the UK and shows what we can achieve as a sovereign trading nation.
'It is a fundamentally liberalising agreement that removes tariffs on all British goods, opens new opportunities for our services providers and tech firms, and makes it easier for our people to travel and work together.
'No deal sets a blueprint for future deals, all trade deals are different and are tailored to the relationships and markets of the countries involved - there is no one size fits all.'
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