Scotland’s food watchdog is being accused of a “cover-up” after it attempted to discredit revelations about the alleged mislabelling of Scottish beef.

The government’s Food Standards Scotland (FSS) denied reports that it was investigating a fraud that could be duping shoppers about the provenance of beef – despite the fact that the reports originated from its own food crime unit.

Critics are accusing FSS of bowing to pressure from the meat industry to avoid damaging a £675 million business. FSS has apologised for causing “confusion” but defends its independence and insists there has been no cover-up.

Scottish beef can attract premium prices around six per cent higher than beef from other countries. But there have been allegations that cheaper beef from Ireland, England or elsewhere in Europe is being illegally repackaged and sold as Scottish.

By committing this kind of fraud, beef businesses can boost their profits by thousands of pounds – and mislead millions of consumers.

Professor Chris Elliott, the expert from Queens University Belfast who led the UK Government’s food fraud review after the horsemeat scandal in 2013, warned that the Scottish beef brand could be targeted by criminals to make money.

He told the Sunday Herald: “There has been some concerns expressed to me from various sources over recent months that some beef labelled as coming from the UK or its regions and on sale in the UK is in fact produce from another country.”

Protecting the Scottish brand was vital, he said. “There seems to be some confusion relating to the investigation, or rather non-investigation, into beef mislabelling in the Scottish industry.”

The intelligence manager of the FSS Scottish Food Crime & Incidents Unit, Duncan Smith, is on record saying that he was investigating reports of mislabelled beef. He called for “whistleblowers” to contact FSS with information on where this was happening.

“We’ve had several reports that this is ongoing by meat processors,” he said. “It’s something we’re very, very interested in trying to get to the bottom of.”

Consumers were “getting duped as to what they are actually buying,” Smith warned. “Chances are that they are paying more money for what they believe to be premium Scottish beef and it’s an inferior type of beef.”

However, FSS later issued a statement saying “there is no current investigation into the Scottish beef industry and no suggestion of any wrongdoing.” It criticised reports of the comments as inaccurate and “sensationalist”.

FSS’s credibility and leadership were questioned by the investigative food journalist and author, Joanna Blythman, who also writes for the Sunday Herald. “It appears that senior staff at FSS are attempting to cover up major food fraud,” she said.

“FSS’s haste to deny the very existence of its investigation and promptly play down any suggestion of wrongdoing suggests that political and/or meat industry pressure has been brought to bear on FSS to slam a lid on the investigation lest it damage the Scotch beef brand.”

Blythman accused FSS of confusing its role as a public watchdog with protecting the commercial interests of Scotland’s food and drink industries. It should be rooting out food fraud, she argued, “but I’m afraid that senior management at FSS is either unwilling, or unable to fulfill this crucial public protection role.”

The Scottish Greens environment spokesman, Mark Ruskell MSP, has lodged questions in the Scottish Parliament asking ministers about the beef mislabelling allegations. “It’s very concerning that there now seem to be contradictory reports coming from the Scottish Food Crime & Incidents Unit and its parent body, Food Standards Scotland,” he said.

“Consumers have a right to know where their food comes from, and this is vitally important to both the domestic and export markets for our world-renowned Scottish meat industry.”

FSS chief executive, Geoff Ogle, stressed there was no threat to public safety. “Consumer trust is vital and we regard our independence as essential to retaining that trust,” he said. “Any suggestion of a cover up is just wrong.”

The FSS crime unit had received “a small number of anonymous reports of beef mislabelled as Scottish”. They were being assessed to see whether or not a formal investigation should be launched.

There was a “clear separation between intelligence and information received and formal investigation”, according to FSS. “The fact that we have information and are looking in to it does not constitute an investigation.”

Reports of potential food fraud did “not necessarily mean that there is a widespread problem,” FSS told the Sunday Herald. “In the case of reports we have received regarding Scottish beef it should not have been presented as such.”

Ogle accepted that FSS had caused misunderstandings. “We would like to apologise if there has been any confusion,” he said. “Ultimately, we accept that we weren’t clear enough ... and it is incumbent on us to correct any misunderstanding, which we have done.”

The National Farmers Union in Scotland described reports of beef mislabelling as “alarming”, but welcomed “clarification” from FSS. “Were any illegal activity to come to the attention of FSS which could undermine the efforts of primary producers in Scotland, then we would want the food crime unit to act,” said the union’s communications director, Bob Carruth.

The trade body, Quality Meat Scotland, understood that FSS was “looking into the credibility of some claims of poor practice”. But there was “no suggestion of a formal investigation or actual wrong-doing”, said its chairman Jim McLaren.

“If at any time the FSS crime unit has any evidence that any isolated case of poor practice is taking place they will have our industry’s 100 per cent support that action is taken very quickly to stamp this out.”

The Scottish Beef Association, which represents producers, cautioned that there was always a potential for stories about fraud. “We have the utmost confidence in FSS, Quality Meat Scotland and the meat wholesalers to deliver what the public expects,” said the association’s chairman, Neil McCorkindale.

The Scottish Government pointed out that it had set up the FSS crime unit in the wake of the 2013 horsemeat scandal to tackle food fraud. “We are committed to preserving the excellent reputation of Scottish beef as a brand that is recognised and trusted around the world and we take the issue of fraudulent labelling very seriously,” said a government spokesman.