In 2017, emergency measures were introduced on nearby Loch Carron after a dredger caused significant damage to a large flame shell reef.
The reef had been discovered five years earlier and was estimated to contain about 250 million flame shells.
Subsequent dives to the seabed revealed the extent of the damage but the skipper involved had legally done nothing wrong because the site contained no restrictions.
That wasn’t the case though at Loch Alsh where an MPA has been in place since 2014.
One of the boats involved in the Loch Alsh incident, the Dawn Maid, is part owned by Mull-based businessman Calum MacLachlainn.
He told BBC Scotland news that he wanted answers from Marine Scotland on why his skipper was given incorrect information by fisheries officers.
He added: “Both skippers involved acted on advice given to them.
“I was told a number of years ago by Marine Scotland to check with local fishery officers if there was any ambiguity at all.”
Mr MacLachlainn said he would welcome a discussion with the fisheries authority.
The Scottish government confirmed it had received a report of illegal fishing, adding: “We can confirm we are investigating an incident in the Loch Alsh area over the weekend.”
The spokesperson was asked specifically about reports that fishermen had been given incorrect information to which they added: “As this is a live investigation the Scottish Government is not able to comment further.”