Scottish salmon farmers will be allowed to create supersized farms in return for accepting much stricter controls on parasites and marine pollution.

The Scottish Environment Protection Agency (Sepa) has said it will no longer restrict the size of salmon farms as long as they meet tougher standards limiting chemical, faecal and organic waste pollution in surrounding seas.

Scottish ministers have also unveiled much stricter legal limits on the level of sea lice allowed on farmed fish, amid mounting anger about plagues of sea lice, a parasite that eats fish alive, killing wild Atlantic salmon.

The new measures are expected to see much larger farms placed in deeper water further off the Scottish coast, in part to replace smaller inshore fish farms that may be forced to move because of the tougher pollution tests.

At present fish farms have a ceiling of 2,500 tonnes of fish per site. That will no longer apply, but larger firms will only be authorised in areas that are more “exposed, more remote, deep-water locations with strong tides”, said Sepa.

Deeper open seas should lead to their waste – medicines and chemicals used to control disease and lice, fish faeces, and uneaten food – being much more quickly dispersed and less likely to pollute the seabed. However, deep sea sites are at much greater risk of storm damage and of bad weather preventing visits by fish farm workers.

Fergus Ewing, the Scottish rural affairs minister, told Holyrood on Wednesday he would introduce legislation next year that would require fish farms to report sea lice levels every week, and for those figures to be published.

At the same time, the trigger for reporting sea lice incidents will be progressively lowered, first from three lice per fish down to an average of two, with the trigger for enforcement action falling from eight lice per fish down to four.

This would allow earlier intervention and enforcement action, Ewing said. “These new measures signal a major shift from self- to statutory regulation,” he told MSPs.

Conservationists and anglers say fish farms act as factories for sea lice, which in turn feed on wild Atlantic salmon swimming past, with many calling for a ban on new farms. The number of wild salmon caught by Scottish anglers last year plunged to the lowest in 70 years.

The Scottish salmon farming industry, which is largely owned by Norwegian multi-national companies who are under investigation by the European commission for alleged price fixing, want to double production by 2030, by up to 400,000 tonnes.

Holyrood’s environment committee warned last year that goal would be “unsustainable and may cause irrecoverable damage to the environment” unless pollution and parasite controls significantly improved.

Mark Ruskell, the Scottish Green party’s environment spokesman, called for an urgent review of existing fish farms to make sure they met Sepa’s new standards, with greater emphasis on animal welfare.

“There are real fears that the industry’s plans to double annual production will cause needless suffering to millions of fish,” he said.

Julie Hesketh-Laird, chief executive of the Scottish Salmon Producers Organisation, said the new Sepa policy would help much larger farms develop in deeper waters but admitted to fears inshore that farms could be forced out.

“However, the SSPO is also adamant that no farm that is performing well in an inshore location should be forced to move to a deeper, offshore site. The new regime should be flexible enough to accommodate best practice everywhere,” she added.