The licensing of salmon farms by the Soil Association has led to some within the UK's organic movement to voice concerns that standards are slipping.
The study highlights the possibility some fish could escape
A confidential study for the UK's top organic body highlighted gaps between its principles and the standards it accepted, BBC Newsnight reported.
The study said farmed fish could escape and carry sea lice, and waste from fish farms was not captured or recycled.
The Soil Association said backing fish farms did not undermine its standards.
One of the first salmon farms to be fully recognised as organic by the Soil Association is situated on the remote islands of the Outer Hebrides.
The farm's owner, Angus MacMillan, said that it did meet the organic benchmark of being sustainably produced in as natural conditions as possible.
He said the salmon were fed natural food and the cages, which held half as many fish as conventional farms, were located in deep, tidal waters.
"Half of the world's sea food is now being farmed," Mr MacMillan told Newsnight reporter Liz MacKean. "In order to have sea food available to consumers, it has to come from aquaculture."
But purists argued that the only kind of organic fish were wild ones. Lawrence Woodward, former chairman of the Soil Association's standards committee, believed the decision to license the farms was a mistake.
"Salmon farming in cages has nothing at all to do with organic principles," he said.
"It is very regrettable that the Soil Association has gone down this line of trying to certify something that is so distant from the principles."
The association's director, Patrick Holden, defended the decision.
"It is about drawing a line and delivering a realistic compromise between the ideal system, which is wild, and a system that works within the principles of sustainable agriculture but delivers the volume of food that people need," Mr Holden argued.
"Given that the oceans have been so seriously depleted, we thought that this was an area we should be involved in."
He added: "The high principles upon which the Soil Association was founded 60 years ago are as intact today as they ever were."