The amount of fish that can be caught in Europe within scientifically recommended levels inched upwards under a deal made in Brussels on Wednesday, but campaigners said the agreement still marked only "tepid" progress towards sustainable fishing.
About 80% of Mediterranean and 47% of Atlantic stocks are over-fished, European Commission figures show.
The European Parliament on 6 February 2013 overwhelmingly backed reform to end decades of over-fishing and restore EU sea stocks to healthy levels by 2020.
The European Council agreed to the reform of the Common Fisheries Policy in May.
The Common Fisheries Policy, which dates back to the 1970s, is widely regarded as a failure. It has allowed subsidised, industrial-sized fleets to devastate fish stocks, while eurosceptics have scorned it as bureaucratic.
The revised policy, to take effect in 2014, is designed to enforce sustainable catch limits.
European ministers who have been negotiating since Monday on fish quotas agreed that 27 of the 50 stocks that scientists provide advice on would be fished at sustainable yields in 2014, up from 25 in 2013. It is the last time quotas will be agreed in this way, with new reforms coming into force next year.
The EU's fisheries commissioner, Maria Damanaki, said the meeting had pre-emptively adopted the conservationist spirit of the reforms that will guide quotas from 2015 onwards.
"I would like to say to you that I'm really very happy, because this year the ministers they have decided to implement the reform in advance," said Damanaki. "So the new fisheries policy is already here. All the components of the new reform are already here.
"When the [population] trend is stable or positive, we will be able to have small increases [in catch limits]. When the trend was going down I have insisted that we need to reduce the quotas and the council has done that."
Green groups said the results from the meeting showed improvement, but there was little to indicate member states had voluntarily embraced sustainability.
Xavier Pastor, executive director of Oceana in Europe, described the council's stance as "tepid".
"Whereas the council has made progress by adopting certain catch limits that will increase the number of stocks exploited at MSY [maximum sustainable yield] levels to 30, it is regrettable that 46% of stocks will remain exploited beyond the sustainable limits recommended by scientists, a figure similar to 2013."
The annual meeting on catch quotas, designed to ensure Europe's stocks are sustainably fished, has typically seen fish populations losing out to economic and political interests. Between 1987 and 2011, the average total allowable catch (TAC) set by the EU was 33% higher than levels recommended by scientists.
Under the reforms to the Common Fisheries Policy passed last week, ministers will in future be required to adhere to advice from conservation scientists when setting quotas. The reforms also banned fish discards – the practice of throwing back fish caught in excess of their quota.
Britt Groosman from the Environmental Defence Fund said: "This year's council meeting results are not a good indicator of the likely success of the reformed CFP. First of all because the new CFP is not yet in place, and it is thus to be expected for member states to try and continue their short-sighted battle to lobby for higher TACs for their own fleets."
UK fisheries minister, George Eustice, had gone into the meeting saying that to avoid excessive discarding, many stocks would need to be fished above MSY until the discard ban comes into effect in 2015.
Eustice was also under pressure from the fishing industry to ensure fishing fleets' days at sea were not cut. He said the negotiations had been "difficult".
"I am pleased that we were able to secure the best possible deal for ensuring sustainable fisheries and a strong UK fishing industry. It was my top priority to ensure that days at sea for fishermen would remain the same next year and that is exactly what has been achieved."