The Federal Agriculture Department has been ordered to investigate whether money was offered to whistleblowers in the live export industry in exchange for vision of cruel conditions onboard a ship bound for the Middle East.

Key points: The footage showed dead or dying sheep onboard a ship to the Middle East

The footage showed dead or dying sheep onboard a ship to the Middle East Agriculture Minister David Littleproud wants to investigate how the clip was obtained

Agriculture Minister David Littleproud wants to investigate how the clip was obtained The clip led to several reviews of the trade and a temporary industry-imposed ban

Agriculture Minister David Littleproud wants his department to investigate how the footage, taken on board the Awassi Express between May and October 2017, was obtained.

It comes after media reports published allegations that footage showing sheep in distress was paid for by animal activists as part of a campaign to ban the trade.

The ABC has not verified the claims or been able to contact the whistleblower at the centre of the campaign.

Footage showing dead and dying sheep onboard a ship bound for the Middle East made public in April last year has led to several reviews of the trade and a temporary industry-imposed ban.

Mr Littleproud said the Agriculture Department had already investigated more than 800 pieces of footage, "but it couldn't hurt to investigate more".

"Depending on the outcome of these investigations, we may need to consider the best way to make sure taking action which could reasonably be expected to cause cruelty to animals being exported is punishable," Mr Littleproud said.

"We need to make sure all animal cruelty is stamped out regardless of the motivation behind it."

The Awassi Express was at the centre of the live export animal welfare allegation. ( ABC News: Nicolas Perpitch )

The decision to formally investigate the way in which the footage was obtained came after Deputy Prime Minister Michael McCormack said the Government would "look into it".

Before Mr Littleproud called the investigation, Animals Australia issued a statement saying it had also called on the department.

"Animals Australia stands behind the evidence and has today (Monday) written to the Department of Agriculture to voice its strong concern as to the way whistleblowers expose the abhorrent treatment," it said.

"Recent Parliamentary Committee recommendations into improving whistleblower protections in Australia sought to address exactly this victimisation and recommended that more needs to be done to compensate and protect whistleblowers.

"Animals Australia calls for any evidence to be provided in full to the department as the relevant regulator."

Last week, National Farmers Federation president Fiona Simson expressed concern about reports that payment had been exchanged for footage.

"When a cash reward is offered, it can act as an incentive to potentially misrepresent or manufacture circumstances where animals are indeed suffering," Ms Simson said.