A decision by a nonprofit organization to certify a company’s Antarctic krill harvesting has drawn fierce criticism from conservationists and undercut the group’s image as a diligent steward of ocean fishing stocks.

Krill, tiny pink shrimplike organisms that dwell in vast schools, are an essential link in the Antarctic food chain, a food source for penguins, seals and many species of whales in the Southern Ocean. Fisheries have harvested krill as food for farm-raised salmon and for its oil, rich in omega-3 acids, used in human dietary supplements.

Last month the 15-year-old Marine Stewardship Council certified the krill fishing of the Norwegian company Aker BioMarine as environmentally sustainable. In essence, it said that the operation was in keeping with its core principles — namely, that fisheries must maintain a healthy population, must not damage the ecosystem and must be effectively managed.

Gerald Leape, director of the Pew Environment Group’s nonprofit Antarctic Krill Conservation Project, said that the council "ignored irrefutable evidence" of threats to the Antarctic ecosystem in granting the certification, which gives Aker BioMarine the right to label its krill-oil pills with the council’s blue logo.

No one is suggesting that krill stocks are in imminent danger of extinction. But opponents of certification say that scientific data on the fishery’s impact are lacking and that the council’s decision is thus based on guesswork rather than on research into the long-term effects.

Even if the fishery is healthy now, they argue, the Marine Stewardship Council is encouraging fishers to exploit the Antarctic ecosystem, which already faces an uncertain future because of its retreating ice pack and acidification.

Casson Trenor, a Greenpeace campaigner, wrote that the council had given "an unofficial nod to the basic idea that vacuuming up the tiny life forms forming the foundations of the oceanic ecosystem is an acceptable practice."

The council counters that the harvest — at 150,000 tons in the 2007-8 fishing season –amounts to less than 1 percent of total estimated krill biomass for the area.

There seems to be at least a grudging acknowledgment that Aker BioMarine’s fishery — which is a single, technologically sophisticated ship — is relatively well run. But opponents say that the council should have looked at the overall impact of krill fishing, and not just assessed one company.

Some of the friction comes from a growing sense among the council’s critics that no industrial fishery can really be sustainable. The U.N. Food and Agriculture Organization warned last year that 80 percent of the oceans’ commercial fish stocks were either being fished at maximum limits or were overexploited.

"If you had asked me a few years ago, I’d have said the MSC was better than nothing," said Jennifer Jacquet, a postdoctoral researcher at the University of British Columbia Fisheries Center who has studied marine eco-labeling. "Today, I’m skeptical."

The Marine Stewardship Council was founded in 1995 by the World Wildlife Fund and Unilever, then a big seafood retailer, to encourage stores, restaurants and consumers to choose fish harvested in responsible ways. Under the council’s system, third-party contractors assess the fisheries at a cost ranging from $20,000 to more than $100,000 and recommend whether they should be certified before the council acts. The fisheries also undergo annual audits and seek recertification every five years.

So far the council has certified 86 fisheries around the globe and more than 5,000 seafood products. No fishery has ever been denied certification by the council once it was recommended for it, although adjudicators have regularly required remedial action.

Yet some scientists argue that the council’s pledge that that certified products come from — and can be traced back to — a sustainable fishery does not hold up well to scrutiny.

Last fall there was an outcry over the certification of the Pacific hake fishery off the coast of British Columbia and the United States. The move was strongly opposed by the Monterey Bay Aquarium in California and by Oceana, a conservation group. They cited studies showing that stocks of the fish, also known as Pacific whiting, had fallen by 89 percent since the mid-1980s.

The council replied that an independent team of scientists had found that the fishery met its standard and that the finding had been supported by an independent adjudicator.

Sidney Holt, an expert on fish population dynamics who helped the council write its basic principles in the 1990s, said he had become "extremely unhappy" with the organization.

The problem, he said, was that the outsourcing of fishery assessments to commercial contractors paid by the fisheries created a conflict of interest because the contractors had an incentive to present the science in a way most flattering to the fishery. "It’s like having the prosecutor in court appoint the judge," he said.

But Mike Sutton, a founder of the council who is now director of the Center for the Future of the Oceans at the Monterey Bay Aquarium, said that argument was "absolute nonsense."

"The truth is that somebody’s got to pay for certification," just as companies pay auditors to certify their books, he said.

In another controversial Antarctic case, an independent adjudicator sent an assessment back to a company for reconsideration after it recommended certification for the Ross Sea toothfish, marketed in the United States as Chilean sea bass. Scientists had accused Moody Marine, the company that carried out the stock assessment, of ignoring unfavorable data.

Asked about possible conflicts of interest in certifying fisheries, an official from Moody Marine, Andrew Hough, said, "We base our reputation on independence and impartiality."

James Barnes, executive director of the Antarctic and Southern Ocean Coalition, an environmental group, said that in the toothfish case, about 25 international scientists with decades of Ross Sea experience had strongly opposed certification, but "were slapped aside as though they were schoolboys."

Kerry Coughlin, the Marine Stewardship Council’s regional director for the Americas, said that certification had been recommended over the objections of some scientists, but not all.

Some of the criticisms are being registered in the marketplace. For example, Whole Foods Markets has said it will no longer sell krill-oil supplements, logo or no logo. Sutton, the council founder who now works at the Monterey Bay Aquarium, said it was essential for the fishing industry to work with conservationists if it wanted to effect change because "market-based initiatives have more impact than government regulators ever will."

"It seems to me that it’s doing exactly what it was intended to do," he said of the council, "and that is, move the whole industry closer to sustainability."