Conservation groups and some governments had argued for a ban on bottom-trawling, which drags heavy nets and crushing rollers on the sea floor.
Negotiators could only agree on a limited set of precautionary measures.
Last month, leading scientists warned there would be no sea fish left in 50 years if current practices continued.
Negotiations at the UN in New York aimed to secure an agreement to go before the General Assembly next month.
Slow growth
Central to discussions was bottom-trawling, widely regarded as a destructive fishing practice.
"The final agreement has more loopholes in it than a fisherman's sweater,"
It targets slow-growing species such as orange roughy, which take decades to reach breeding age. Such species are especially vulnerable to overfishing because the population replenishes itself very slowly.
For three years, conservation groups have been pushing for a UN moratorium on bottom-trawling; for the third year running, they have been disappointed.
"We had been hoping the amazing creatures and habitats of the deep sea would get an early Christmas present this week," said Bryce Beukers-Stewart, fisheries policy officer with the Marine Conservation Society.
"But once again, short-term political and economic interests have over-ridden common sense."
Bottoming out
Eleven nations have bottom-trawling fleets, with Spain's being the biggest. Studies have indicated that none would be commercially viable without government subsidies.
In 2004, a report compiled for the World Conservation Union (IUCN) and other environmental groups concluded that bottom-trawling was "...highly destructive to the biodiversity associated with seamounts and deep-sea coral ecosystems and... likely to pose significant risks to this biodiversity, including the risk of species extinction."
Sea fish 'gone in 50 years'
In the same year, 1,100 scientists put their names to a petition supporting the demand for a moratorium.
All this scientific evidence could not convince enough UN delegates that a moratorium was needed.
The eventual deal which goes forward to the General Assembly mandates governments to adopt unilateral "precautionary measures" to ensure their bottom-trawlers do not cause significant damage to marine ecosystems.
In areas covered by Regional Fisheries Management Organisations (RFMOs), "precautionary measures" must be established by the end of 2008.
"The final agreement has more loopholes in it than a fisherman's sweater," fumed Greenpeace oceans policy advisor Karen Sack.
Conservation groups accused Iceland in particular of blocking further protection. Iceland is already under fire from the conservation lobby over its recent decision to resume commercial whaling.
"The international community should be outraged that Iceland could almost single-handedly sink deep-sea protection and the food security of future generations," said Ms Sack.
Last month, an international team of scientists, having compiled a vast range of data from a wide variety of sources, warned that at current rates of depletion, there would be no viable populations of fish left in the seas by the middle of the century.
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