The company has denied any wrongdoings.
It is BBC that reveals that Mowi and several other companies are under investigation by Scottish Environment Protection Agency (Sepa) for possible misreporting of chemical use.
Mowi produces up to 60,000 tonnes of salmon in the UK each year.
Mowi’s head of communications, Ian Roberts, said: “We have confidence in what we’re reporting for medications, it is used sparingly.
“We, of course, vaccinate our fish to protect them from fish health challenges,” he continued.
According to BBC the Scottish regulators is increasing its inspections across the salmon industry and tougher approach is expected. New guidelines on salmon farming will be published within two weeks.
“If companies do the right thing, then they have nothing to worry about.
If companies do the wrong thing, we are there to find that out and make sure they improve their game. If that’s going to take tough action, you can be assured we’ll take it,” said Sepa chief executive, Terry A’Hearn.