Thomas Jones says the hand picking of mussels in the Conwy estuary may end with the closure of his plant.But Conwy council said it has had to make numerous visits to the plant to offer "substantial" food safety advice.
It said that despite this the plant had "made enough progress" to stay open.
Mussel gathering has existed on the estuary since Roman times and is one of the few places where the mussels are still hand raked from the river bed.
The plant, on the quayside in Conwy, takes mussels from the estuary and treats them for 48 hours to remove any harmful bacteria.
But Mr Jones said Conwy environmental health officials have visited the mussel plant 44 times during the season, which runs from September to April.
He said the mussels remain safe to eat but officials raised concerns about the quality of the river water being used to treat them, even though he said the levels of bacteria were well below permitted limits.
He said: "This industry has been going for hundreds of years.
"I'm the fourth generation of our family to work in mussel fishing, and it's extremely upsetting that all our hard work is being ended in this way.
"There's nothing wrong with our product. The reason that we're closing isn't because of the quality of the mussels.
"They're not treating us fairly in comparison with other businesses in the food industry. No-one else gets the same level of scrutiny as we've been having."
Six men are currently fishing for mussels in Conwy, though not all of their catch is processed in the town.
Conwy council said its food safety officers had offered a substantial amount of advice and guidance to the business so it could comply with food safety laws.
"Unfortunately, the business has been slow to alter its practices and systems sufficiently to fully comply with the rules that are there to minimise the risk to public safety," it said in a statement.
'Professional manner'
"However, the business had made enough progress by this week for the council to agree it could to remain open.
"It is regrettable that the business has chosen to close, but public safety has to take priority.
"We do not accept that the council's officers have been over-zealous. They have been going about their work, as ever, in a professional manner.
"Unfortunately, it is sometimes the case that businesses who fail to comply with rules and regulations seek to blame those who enforce the rules on behalf of the public, rather than take responsibility for their own actions or inactions."
