US Secretary of State John Kerry vowed to keep up the battle to set up a sanctuary to protect the unique marine ecosystem in parts of the Antarctic.
And he voiced "regret" that attempts to create the world's largest ocean sanctuary in the Ross Sea were blocked, with environmental groups accusing Russia of raising objections to the move.
Australia and New Zealand also said they were deeply disappointed, but vowed to push ahead.
"There's simply no comprehensive effort to protect Earth's most critical resource that doesn't include an equally comprehensive effort to create marine protected areas," Kerry, who is on a visit to Jordan, said in a statement.
"The Ross Sea is a natural laboratory. Its ecosystem is as diverse as it is productive, and we have a responsibility to protect it as environmental stewards-just as we do the rest of the ocean."
Three days of talks in Bremerhaven, northern Germany, had gathered 24 nations plus the European Union (EU) in the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR), a 31-year-old treaty tasked with overseeing conservation and sustainable exploitation of the Southern Ocean.
One proposal for a marine sanctuary, floated by the United States and New Zealand, covered 1.6 million square kilometers (640,000 square miles) of the Ross Sea, the deep bay on Antarctica's Pacific side.
The other backed by Australia, France and the EU, would protect 1.9 million square kilometers of coastal seas off East Antarctica, on the frozen continent's Indian Ocean side.
But representatives at the talks said Russia questioned the meeting's legal right to create such sanctuaries.
The waters around Antarctica are home to some 16,000 known species, including whales, seals, albatrosses and penguins, as well as unique species of fish, sponges and worms that are bioluminescent or produce their own natural anti-freeze to survive in the region's chilly waters.
Kerry said "a tremendous amount of work has gone into developing the science that underpins our joint proposal."
"To leverage action, we'll be doubling down on sharing the findings of our scientists who spend those critical months in the dead of winter at McMurdo Station researching and understanding the realties that face all of us."
Although "the road has been harder than we hoped," the top US diplomat said he was pleased so many countries had been able to find common ground and "were willing to work together towards this crucial objective."
"We didn't agree on all of the specifics, but there's an emerging consensus that the Antarctic region requires protection," he added. The next CCAMLR meeting is in Hobart, Australia, from October 23.
Explore further: NASA balloons begin flying in Antarctica for 2014 campaign