However, a spokesman for Ardessie refused to confirm or deny allegations made to BBC Scotland last week that it had allowed the use of an illegal treatment to combat sea lice.
Scottish Quality Salmon said it took the decision after an independent investigation into Ardessie Salmon, in Wester Ross, revealed a breach of quality standards.
The ruling means that Ardessie Salmon cannot sell its products under the quality assurance schemes Tartan Quality Mark and French Label Rouge.
The salmon farm has been investigated in the past by the Scottish Environment Protection Agency (Sepa) but no evidence was found of illegal treatments for salmon disease.
However, a spokesman for Ardessie refused to confirm or deny allegations made to BBC Scotland last week that it had allowed the use of an illegal treatment to combat sea lice.
After the revelations by former fish farm worker Jonathan Davis, SQS chairman Lord Lindsay, said the the body "utterly condemned" bad practice.
Announcing the expulsion of the salmon farm, he said: "An independent investigation undertaken by Food Certification Scotland found that a breach of its quality standards had occurred which resulted in the removal of Ardessie Salmon's Certificate of Approval.
"The company is, therefore, no longer eligible to be a member of Scottish Quality Salmon. The decision is effective immediately."
No indication was given about the details of the "malpractice".
Sea lice
Jonathan Davis alleged that a chemical with the brand name of Deosect was used on the farm, where he worked for three years, to combat sea lice.
The parasites kill salmon and have been a major problem for the industry.
However, the chemical was designed for use in horses and chickens.
Campaigners said the treatment was more lethal to the marine environment than sheep dip and called for tighter regulations.
Mr Davis, now an ecology student, said he knew it was a pesticide but did not find out until later that it should not have been used on fish.
The farm's owner had not denied using the chemical but said an investigation by Sepa did not substantiate earlier allegations by another employee.
Friends of the Earth Scotland said it "warmly welcomed" the expulsion move.
Director, Kevin Dunion, said: "This is tremendous news and is a complete vindication of our position.
"Scottish Quality Salmon are to be congratulated for taking swift and decisive action.
"The decision to expel Ardessie Salmon should act as a shot across the bows of all other fish farmers currently flouting the law or considering doing so."