The artisan cheese company, based in Carnwath, near Lanark, said it faced complete closure unless it was allowed to restart production and resume sale of its existing stock.
FSS had ordered the remaining Dunsyre Blue to be destroyed after it claimed tests revealed the cheese was the source of an E.coli outbreak. The July E.coli outbreak led to the death of a three-year-old girl.
The company denied it was responsible. Last week, it won a battle to keep £20,000 of stock after the FSS withdrew an order to destroy all the remaining cheese.
Workforce laid off
The company said it had already had been forced to lay off its 12-strong workforce. The firm added that £350,000 worth of cheese, currently being stored at its premises, might have to be destroyed if sales were delayed so long that it became overripe.
Company founder Humphrey Errington said: “We are therefore continuing to seek a judicial review at the Court of Session in order that FSS evidence is made public and open to scrutiny.
“We are acutely conscious that a child has died due to the E.coli outbreak over the summer. Our products are being linked to this outbreak by FSS but it has so far failed to provide us with any evidence to support this.
“We have carried out our own tests using leading laboratories in the UK and Europe and found no trace of E.coli 0157.”
He said that FSS could take six months to finalise its report, which would mean all of its cheeses would have to be destroyed and would mean the end of the business.
Unpasteurised cheese
Errington said he believed the FSS has also taken a position against the production of unpasteurised milk cheese.
He added: “This puts the reputation and future of the whole British artisan cheese industry under threat. We have the irony of unpasteurised French cheeses such as Roquefort being imported into Scotland and freely available for sale while a ban exists on our own indigenous cheese.
A spokesman for the FSS said: “FSS does not place any restriction on the use of unpasteurised milk in cheese production provided that the milk, and the production method used, meets legal requirements and does not present a risk to public health."
The FSS confirmed that a petition for judicial review had been lodged but said it could could not comment further on live litigation.