The deal will underpin the ambitious reform of the Common Fisheries Policy (CFP) - in particular dealing with the challenges of discards, maximum sustainable yield (msy) and providing investment in fragile coastal communities - and will now be negotiated between the EU Presidency, the EU Commission and the EU Parliament.
The Scottish Government will now seek to negotiate an increase in Scotland's share of the total UK-level pot from the current 40 per cent to a figure that reflects the fact that the greater share of both industries – 61 per cent of sea fisheries and 86 per cent of aquaculture sales by volume - within the UK are based in Scotland.
Speaking immediately after talks concluded in Brussels, Scotland’s Environment and Climate Change Minister Paul Wheelhouse said: "Tonight was an important first step towards securing a fair level of funding for Scotland's fishing and aquaculture sectors through the new European Maritime Fisheries Fund (EMFF).
"We will now turn our focus to negotiating with the UK Government to try and secure an increased settlement in terms of allocation from the UK pot.
"With well over half of the UK's sea fisheries and almost 90 per cent of aquaculture sales by volume coming from Scotland, a settlement of 40 per cent – which is what we have currently - is unacceptable and should not happen again.
"Scotland's hard working fishermen and fish-farmers deserve a better deal than that. They deserve a deal that is fair and reflects the fact Scotland has the lion's share within the UK of both of these very valuable sectors."
During today's EU Council the Commission also confirmed that trade measures against Faroe Islands on Atlanto-Scandian Herring (ASH) will be implemented at the end of this month unless they cease fishing for ASH and bring forward a suitable plan for sustainable fishing of the stock. Due to on-going pressure from Scotland and some key Member States, the Commission also confirmed they will now bring forward similar measures against Iceland on mackerel. These measures will be outlined to Member States in due course.
Commenting on the progress Mr Wheelhouse said: "Today's progress on trade measures against both Faroe Islands and Iceland will be welcome news for Scotland's fishermen. For far too long the unsustainable fishing of both these nations has gone un-checked and our fishermen, who have been fishing sustainably, have been paying the price.
"Mackerel is Scotland's most valuable fish stock and it is important for the health of our fishing industry as well as the health of the fish stocks that the reckless plundering of the stock comes to an end."