British fishing fleets will be able to land more fish, but face fewer days at sea, following talks in Brussels.
The British government says it achieved victory for the UK fishing industry in the annual EU negotiations, which ended at 04:00 GMT on Saturday.
The Scottish government was less happy, saying it faced “huge frustration”.
The BBC’s Andy Moore says Britain had French and German support in battling against cuts that could have been disastrous for the UK fishing fleet.
One of the proposals was to cut cod fishermen’s days at sea to just four a fortnight.
That particular threat now seems to have been lifted.
But boats will be confined to ports for longer making it harder to cash in on rises in fish quotas and Scottish Fisheries Minister Richard Lochhead said big challenges remain.
Bertie Armstrong, chief executive of the Scottish Fishermen’s Federation, criticised the cuts in days at sea, which is estimated to be between 15% and 25%.
He said: “While fishing opportunity in terms of tonnage has always been vital, this time around it was the granting of enough time at sea to actually catch the fish that was under threat.
“This is a bitter blow for our fishing fleet, which is now going to struggle to maintain economic viability under the impact of these totally unwarranted cuts.”
The UK government’s fisheries minister Richard Benyon said allowable catches for a number of species would go up next year.
Fishermen in the north-east of England, for example, will be able to double their quota of herring.
The amount of haddock that can be caught off the west coast of Scotland will treble.
Our correspondent says some fishing stocks in some areas have recovered well, but it is a mixed and complicated picture.
The European Fisheries Commission was seeking an overall reduction of 11% for the total catch in the Atlantic and North Sea.
Many conservation groups say big reductions are needed to protect fish stocks.
The exact details of how many days each boat can take to the sea will be worked out over the next few weeks.
Mr Benyon said: “After two days of tense and frustrating negotiations, I am delighted to have secured the best deal possible for the UK fishing industry and ensure the future sustainability of our fish stocks.
“By arguing that we should follow scientific advice, we have been able to agree quotas that will not only allow local fishermen to make a living but will also ensure that we can protect the environment.”
Mr Lochhead said: “Quotas are the lifeblood of the fleet and we have won increases for our key stocks in line with the science.
“There is very good news on the west coast in particular with a 200% increase in haddock quota and the removal of regulations that were hurting the fleet.”
He also highlighted the retention of this year’s scampi catch allowance in Northern Ireland next year.
But he added: “We are very disappointed that despite the call from many member states for a pause in the annual cut in days at sea for vessels that fish in the Cod Recovery Zone, Europe pressed ahead.”
The Scottish government was particularly delighted that the EU Commissioner, Maria Damanaki, accepted Scotland’s interpretation of article 13 of the Cod Recovery Plan.
This allows for boats to fish if they are practicising “cod avoidance measures”, such as eliminator trawls, which allow effective fishing for haddock and whiting while eliminating cod from the catch.
The agreement came only hours after 17 skippers from the Shetlands were ordered to hand over almost