BBCNewsScotland reports that anglers and landowners have claimed that parasites from farms are at least partly to blame for declines in wild salmon and sea trout.
The Scottish government may now follow the example of Norway and restrict the spread of farms.
The fish farming industry said there was no evidence that parasites were threatening wild fish stocks.
Environment Minister, Stewart Stevenson, revealed he is considering forcing salmon farmers to publish information about lice levels on specific farms, a measure which has been called for by critics of the fish farm industry and which has been implemented by the Norwegian government.
However, Steve Bracken from Marine Harvest, Scotland's largest salmon producer, said there was not enough evidence to suggest that parasites - known as sea lice - were responsible for any declines in wild fish stocks.
He argued producers should not be forced out of existing farming areas.
"We can't say that we're not having an impact. It's just knowing how much of an impact we've got," he said.
"And that's why I think it would be wrong to say 'well, we don't know, we don't really like this but we think you should go out of the loch'. We don't think that's a reason for moving."
The BBC Scotland Investigates: Scotland's Fishy Secrets programme also examined whether lice have become resistant to the range of chemicals being used to treat them and revealed evidence that the industry may be hiding the scale of problems it has encountered in treating the parasites.
The group which represents salmon farms in Scotland said the industry was not concealing information from regulatory authorities.
Scott Lansburgh, chief executive of the Scottish Salmon Producer's Organisation, said: "We're regulated by the environmental protection agency, SEPA.
"So they keep a close eye on what's going on in the industry as do the fish health inspectorate and their reports are open to all to see and we're regularly reported on and we're regularly inspected so we're not hiding anything."
Mr Landsburgh also commented: "I am very angry that this proposition has been put forward. It is ludicrous to suggest that fish farms could be banned. Salmon farming has always developed on the west coast and in the Northern and Western Isles where conditions are ideal and away from where 90 per cent of all wild salmon in Scotland are caught."
"There is no empirical evidence to link salmon farming with declines of wild salmon on the west coast. International declines are seen throughout the North Atlantic in areas where there are no salmon farms."
Environment Minister Mr Stevenson also commented, saying: "At the moment there isn't evidence of resistance to the various treatments there are, some other countries have that resistance if you continuously use the same treatment."
The wild fish lobby said that any resistance could have serious implications.
Guy Linley Adams, a lawyer working for the Salmon and Trout Association, said: "If we're getting resistant sea lice we need to know where the populations of those resistant sea lice are.
"If it does spread we get multiple resistance in sea lice across the west coast of Scotland and in the isles then you've got this awful scenario of farms with huge lice burdens causing problems not just for the farmers but for the wild fish as well."
BBC Scotland Investigates: Scotland's Fishy Secrets will be broadcast on BBC One Scotland at 22:35 on Tuesday 18 October, and then on the programme website.
Coastal Farm Ban Urged To Protect Wild Stocks
SCOTLAND, UK - Fish farming could be banned in some coastal areas in a bid to protect wild fish stocks, BBC Scotland reports. This claim has been met with furious opposition from many Scottish fishery groups.