A federal report on the status of Maine’s wild Atlantic salmon cited aquaculture among the top barriers to the fish’s recovery.

The report, released Tuesday by the National Research Council, rated aquaculture the third-highest concern, below only dams and acid rain.

A complex interaction of myriad factors has led to the salmon’s decline over many decades, with problems ranging from overfishing to water pollution to global warming.

Salmon farming is a relatively recent addition to the mix. But the committee of 13 scientists from across the country who produced the report identified contemporary issues, such as salmon farming, as major barriers to bringing back the struggling population from today’s historic low.

“Salmon farming has the potential to adversely affect salmon populations in Maine genetically and ecologically and might have already done so,” the report said.

As Maine Aquaculture Association spokesman Sebastian Belle pointed out in an interview Wednesday, aquaculture was mentioned only a few times among the dozens of actions suggested by the committee. The report called some aspects of fish farming problematic but did not include it among the most urgent actions – removing dams and reducing acidity.

However, fish farms are known to cause water pollution, as well as spreading disease to wild fish, the report said.

Industry representatives frequently argue that diseases like infectious salmon anemia existed in the wild long before the start of salmon farming. The argument did not convince the committee. Dense populations of fish in farm pens can be a catalyst for disease – regardless of its source, the report said.

The committee also raised concerns that salmon farm escapees can cause problems if they compete or interbreed with wild populations.

The committee reiterated its January 2002 finding, in an interim report, that the salmon in Maine’s rivers are genetically distinct, with noticeable differences from fish native to Europe or Canada. Most aquaculture fish are genetic hybrids, with ancestors from Norway and Canada as well as Maine.

Thus, the committee echoed a frequent worry that escaped aquaculture fish could, over time, breed the remaining populations of wild salmon out of existence, with a deluge of foreign genes.

The primary location of Maine’s aquaculture industry in Cobscook Bay increases concerns, as most of the federally protected salmon rivers empty into the bay near the Canadian border in northern Washington County. The scope of the problem varies, but at a high in 2001, 75 percent of the salmon that were captured returning to the St. Croix River – 58 fish – were aquaculture escapees.

Aquaculture operations frequently point out that little evidence exists to prove that either disease or escaped fish from aquaculture has ever harmed Maine’s wild salmon.

The committee made a point of agreeing. However, the committee added that research that could lead to such findings has simply not been done in Maine.

“There is no reason to believe that the harm to wild fish that has been documented elsewhere could not occur in Maine,” the report said.

The committee recommended a long-term effort to modify salmon farming operations to better prevent the escape of farmed fish. And to give wild fish their best chance, salmon farms that seem to be causing problems should be moved away from wild salmon populations, the report said.

However, the cost of such actions could be so high as to take all the profit out of aquaculture, an industry that is struggling with the financial fallout of disease outbreaks and lawsuits, the report said.

Belle said that Maine has worked cooperatively with state and federal agencies and environmental groups to address escape problems, which were a major concern for the industry a few years ago.

Though new technology and knowledge always creates room for improvement, Belle believes that the present system of containment management plans and third-party audits is doing a good job of keeping farmed fish where they belong.

“I can say with an absolutely straight face that Maine growers are ahead of any in the world,” he said.