British fishing fleets will be able to land more fish, but face fewer days at sea, following EU talks in Brussels.
The British government says it achieved victory for the UK fishing industry in the annual Common Fisheries Policy negotiations, which ended at 04:00 GMT.
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.
The National Federation of Fishermen's Organisations (NFFO) - which represents fishermen in England, Wales and Northern Ireland - claims there are 12,000 fishermen employed on around 7,000 boats in the UK.
The NFFO's chief executive, Barrie Deas, said: "The casual observer would never guess that the stocks advice from the International Council for the Exploration of the Seas for this year paints the most positive picture for more than a decade."
He said the outcome of the "tortuous" negotiations was "absurd" and provided "ample evidence" of the need to reform the Commons Fisheries Policy.
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 practising "cod avoidance measures", such as eliminator trawls, which allow effective fishing for haddock and whiting while eliminating cod from the catch.
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."
Conservation group Oceana Europe said scientific advice had been ignored.
Oceana's executive director Xavier Pastor said: "Unfortunately nobody seems to be looking out for the welfare of the resources.
"This type of short-term approach will lead to the deterioration of not only fish populations, but also of the profitability of the sector and the viability of the fishing communities."
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."
Scottish Conservative MEP Struan Stevenson described the talks as being an "annual circus" akin to a "Christmas pantomime".
He said : "It is the most vivid manifestation of the discredited system of fisheries micro-management from Brussels. Happily we may now be able to sweep this aside with the complete reform of the Common Fisheries Policy that is currently under way."
The agreement came only hours after 17 skippers from the Shetlands were ordered to hand over almost £3m by the High Court in Edinburgh after lying about the size of catches from their boats.
The so-called "black fish" scandal dates from 2003-2005.