An angling organisation has called for one of the two farms at Ardessie in Little Loch Broom, Wester Ross, to be closed and the second to undergo a thorough environmental impact assessment (EIA) after the issue came to light. They are operated by Wester Ross Fisheries.
Since April 2007 councils have had full planning responsibility.
According to Salmon and Trout Association Scotland, in 2009 Marine Scotland recommended planning permission should be "withheld" after an audit in 2002.
The anglers say this was because the two fish farms had a poor record of sea-lice control. But it appears that the Highland Council was not told of the assessment.
Guy Linley-Adams, solicitor to the Salmon and Trout Association Scotland's Aquaculture Campaign, said: "The Highland Council has now been called upon to enforce the condition at Ardessie B and inform the operators that they do not have planning permission for that site."
A Highland Council spokesman said: "The Scottish Government has been asked for clarification as to whether or not planning permission for the principle of fish farm development, will be granted in respect of Ardessie A&B."
But the Scottish Government indicated planning permission was still needed. A spokeswoman said: "In 2009 Marine Scotland commissioned an audit of an EIA. This assessment was completed to inform Scottish Ministers how any potential application should be treated, as no application was received for either of these sites this was not taken further.
"The assessment identified deficiencies and concluded that it was not comprehensive enough for Ministers to consider the farms through the Audit process.
"Should a planning application be received, it will be assessed for eligibility at that time."
Wester Ross Fisheries Ltd responded through its industry body, the Scottish Salmon Producers' Organisation. Chairman, Professor Phil Thomas, said: "The insinuations by S&TA are simply part of their long-running, misguided and counterproductive campaign against fish farming."