Tonnes of fish are discarded by EU-based ships every year
EU ministers have agreed to a 30% increase in next year's fishing quota for North Sea cod, but will reduce catches for several other species.
The quotas are a compromise between environmental groups, who say some fish stocks are on the verge of collapse, and fishermen who fear for their jobs.
Quotas have been increased for cod and plaice in the North Sea, for mackerel, and for west of Scotland monkfish.
The UK said the deal reached would save west of Scotland fishing communities.
The cut in the prawn quota for trawlers operating off western Scotland - the lifeblood of some fishing communities - was less than the 15% the European Commission had demanded.
Fishing crews will have to install new nets which allow threatened species such as cod and hake back into the sea.
The new nets are intended to reduce discards - the common practice of crews throwing fish back into the sea, sometimes dead, because the quotas have already been exceeded.
The deal on quotas followed intense negotiations in Brussels which began on Thursday.
Scottish Fisheries Secretary Richard Lochhead said: "The future of the west coast fishing communities dominated this week's negotiations, and there will be huge relief that proposals to close the grounds have been successfully resisted."
However, he added that "a number of fishermen face a huge challenge in delivering the agreed conservation measures and we will work hard to help them stay viable".
Under the deal, Spanish, Portuguese and French trawlermen will still be unable to fish for anchovies in the Bay of Biscay and eastern Atlantic, after scientific advice suggested that even after four years of closure, the stocks have not yet sufficiently recovered.
There will be quota cuts for cod, herring, haddock and whiting in the North Atlantic, varying between 25 and 42%.
INCREASES FOR UK FISHERIES
30% more North Sea cod
32% more mackerel
13% more North Sea plaice
8% more monkfish off Scottish west coast
Environmental groups welcomed the decision on new fishing gear, especially square mesh panel nets, which make the catch more selective.
WWF said the selective tackle had brought positive results in Scottish fisheries, but insisted that the new EU rules "must be strictly enforced".
The discard reduction measures "could throw a lifeline to depleted cod stocks in the North Sea, and cod and haddock stocks to the west of Scotland," a WWF statement said.
But the environmental lobby group Greenpeace called the new quotas "disastrous".
Greenpeace oceans campaigner Willie Mackenzie said the quotas contradicted scientific advice.
"These catch levels could see an end to North Sea cod," he warned, urging the EU to do "much more... to allow Europe's decimated fisheries to recover - and that includes setting aside large areas, off-limits to commercial fishing, as marine reserves".
Another lobby group, the Shark Alliance, said the EU's failure to halt the fishing of porbeagle and spurdog sharks had "left these critically endangered species at risk".
Thousands of jobs have been lost in Europe's fisheries in the last 10 years - including 4,000 in the UK. The European Commission says fleet overcapacity continues to undermine fish stocks.
But North Sea cod has benefited from a "good 2005 intake of young fish", the Commission says, allowing an increase in catches to be proposed in agreement with Norway.
Some other stocks, such as herring, are "in many areas in an extremely poor condition", the Commission says.
Map shows proportion of fish types which are overfished (red) and types within safe biological limits (blue). Number in circle is number of fish stocks assessed in each region. Circle size corresponds to magnitude of regional catch. Data source: ICES and GFCM (international maritime organisations).