While it is legal for fish to be treated with certain chemicals - mainly to kill disease and sea lice - there are limits to how much can be used. Environmentalists are concerned the chemicals are having a negative effect in lochs around Scotland.
The investigation, carried out by the Scottish Environment Protection Agency (SEPA), follows an alleged inspection of Howi's UK head office - where SEPA is said to have 'removed documents' from the seafood company.
Mowi, which produces up to 60,000 tons of salmon a year in the UK, has denied any wrongdoings, stating it's confident in its use of medications.
"We, of course, vaccinate our fish to protect them from fish health challenges," said Ian Roberts, Head of Communications at Mowi Scotland.
"I wouldn't be doing this if I thought that we had a strong negative impact on the environment. It is farming at the end of the day, so, no matter what you're farming, you have some level of impact. We need to manage these impacts around farms."
SEPA is to publish new guidelines later this month on salmon farming regulation.
"If companies do the right thing, then they have nothing to worry about," said Chief Executive of Sepa, Terry A'Hearn.
"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."