Rural economy secretary Fergus Ewing accused the Conservatives of delivering the worst possible deal for the sector, which will be subject to EU quotas throughout the 21-month transition period but without any British representation in setting them.
Fishing industry leaders accused the UK Government of trading away sovereignty over British waters.
UK-registered boats landed 708,000 tonnes of seafood, worth £775 million into ports in the UK and abroad in 2015.
Scottish vessels accounted for 62 per cent of the quantity of landings by the UK fleet - more than double the English fleet.
Ruth Davidson admitted the terms of the deal fell far short of what the sector had hoped for.
“During these negotiations, we wanted to gain control over our waters from as early as the end of next year,” the Scottish Conservative leader said in a statement.
“The EU was not willing to move on this. That we now have to wait until 2020 to assume full control is an undoubted disappointment. Having spoken to fishing leaders today, I know they are deeply frustrated with this outcome.
“There is no ignoring the fact that this falls short of what they had hoped for in the short-term. I’ve made clear to them that I will continue to do everything in my power to ensure their interests are protected during the implementation period and beyond.
“I am more determined than ever to ensure that this long-term prize for our fishing industry is seized. So I should make it clear today that I will not support a deal as we leave the EU which, over the long-term, fails to deliver that full control over fish stocks and vessel access.”
Mr Ewing hit out at the terms of the deal and the impact could have on Scotland’s fishing industry.
“The Tories have sold out the Scottish fishing industry once again and Ruth Davidson should be shame-faced for her fastest broken Brexit promise yet,” he said.
“Just last week she said “Britain will leave the CFP as of March 2019. Now we know not only will the UK have to abide by CFP rules during the transition period, it will lose the voting rights it has now. The Tories have delivered the worst possible outcome for Scotland’s fishing industry.
“It is outrageous that Ruth Davidson and Michael Gove could have issued such a misleading statement last weekend when they must have known what was about to happen – and they must both now apologise for their broken promise.
“The Tories have demonstrated once again that for them Scottish interests are expendable. They are so arrogant they now think they can do whatever they want to Scotland and get away with it.”
Scottish Fishermen’s Federation chief executive Bertie Armstrong said: “This falls far short of an acceptable deal. We will leave the EU and leave the CFP, but hand back sovereignty over our seas a few seconds later.
“Our fishing communities’ fortunes will still be subject to the whim and largesse of the EU for another two years. Put simply, we do not trust them to look after us.”