Australian news reports have raised “serious allegations” that falsified export documents are putting the live export industry at risk.

The claims surround copies of documents lodged to different authorities over the export and transport of sheep.

Police authorities have launched an investigation into the claims raised this week.

The story stems from a shipment of sheep which was refused permission to unload in Bahrain in 2012.

The sheep were moved to Pakistan while Garry Robinson, who is a director of the Australian Livestock Exporters Council (ALEC), organised the appropriate No Objection Certificates (NOC)

The NOCs were designed to show authorities in Pakistan, Australia and the destination country that the sheep were not diseased or suffering any other health risk.

But according to the ABC’s 7.30 program, there were important differences between copies of the documents, seemingly to appease all relevant authorities that the shipment was above board.

Reports say one NOC had three crucial words added to it – “if for breeding”. The unauthorised amendment was allegedly to circumvent the requirement to meet Pakistan’s listed health rules.

In an email aired during the same story, Mr Robinson says the altered document “has had magic done to it” and warns his colleagues that “we do not want anybody to compare the magic with the original”.

Other documents have been brought to light too, including a Certificate of Australian Origin for the shipment.

There are several major flaws with the certificate, which would normally have been issued by the Freemantle Chamber of Commerce, including the lack of any appropriate stamps and the fact that the reference number has been handwritten.

Agriculture Minister Barnaby Joyce says if the forgery allegations turn out to be true then “it's a criminal act”.

“People who break the Crimes Act will get themselves a criminal conviction and if it's serious enough they will get themselves a stint at Her Majesty's pleasure,” he said.

Mr Robinson worked for the Wellard Group transport company at the time, but has since left to take up a position as general manager for Perth-based exporter Livestock Shipping Services (LSS).

LSS has been the focus of continued complaints by animal welfare advocates. Several groups have claimed LSS repeatedly breached the Australian Exporter Supply Chain Assurance System (ESCAS), which was set up to guide live exports after trade was suspended in 2011.

“The breaches and the sickening cruelty that we have documented in Jordan, the first, second and third time in Gaza in October last year, and again in February this year, are supply chains that are owned and controlled by LSS,” Animals Australia lawyer Shatha Hamade told the program.

After the story was aired on Monday night, ALEC announced Mr Robinson had “voluntarily stepped down” from his position on the council.

“We support the investigation currently being carried out by the Investigations and Enforcement Unit of the Department of Agriculture,” the ALEC statement said.

“Any outcomes or recommendations of this investigation will be closely considered by the industry's peak industry body. Flagrant breaches of the laws governing the trade will not be tolerated.

“A person named tonight in the allegations, Mr Garry Robinson, has voluntarily stepped aside as a Director of ALEC while the allegations are investigated and dealt with. It is important to note that all parties and individuals implicated are due natural justice and procedural fairness during the investigation process.”