The Federal Agriculture Department has suspended shipments of Australian sheep to an abattoir in Qatar over new allegations of animal welfare violations and breaches of supply chain rules.

Key points: New footage shows sheep thrown around in holding pens, beaten with stick

New footage shows sheep thrown around in holding pens, beaten with stick In the 12 months to February 661,000 sheep have been exported to Qatar

In the 12 months to February 661,000 sheep have been exported to Qatar RSPCA has offered to place observers on next sheep shipments

Last week the Nine Network broadcast video of 2,400 sheep that had died of heat stress on board an export ship bound for the Middle East.

On Saturday the Department said it had received new information and vision from advocacy group Animals Australia, raising serious concerns about the abattoir's operations and compliance with the Federal Government's Exporter Supply Chain Assurance System (ESCAS).

"The allegations include apparent on-selling of sheep to private buyers from the approved supply chain, and mishandling of sheep at an ESCAS-approved abattoir in Qatar," the department said in a statement.

"Supply of animals to the abattoir was immediately suspended and any animals already at the abattoir have been removed.

"In effect, this means no further Australian sheep can be transported to or slaughtered at this abattoir."

It is understood the Nine Network has a deal to broadcast more vision which shows sheep being thrown around in the abattoir's holding pens and beaten with a stick.

Figures from Meat and Livestock Australia show Qatar as one of the largest export markets for Australian sheep.

In the 12 months to February, 661,000 sheep had been exported to the Middle Eastern nation.

The Agriculture Department says this is the first complaint about sheep exports to Qatar since the regulatory scheme was introduced in 2011.

Animals Australia has made a series of complaints about the live export trade since the beginning of March, including allegations of "non-compliant handling practices" in the United Arab Emirates and Oman in addition to the current complaint in Qatar.

The Australian Maritime Safety Authority blocked a shipment of 65,000 sheep leaving Fremantle on Monday, amid ongoing animal welfare concerns.

The Awassi Express is the same vessel, operated by Emanuel Exports, linked to the death of 2,400 sheep last August.

Earlier this week, Agriculture Minister David Littleproud argued a thorough investigation of the capabilities of the live export regulator would be undertaken in the wake of the scandal, but resisted calls for a live export ban.

RPSCA offers to place independent observers on ships

The RSPCA has offered to place independent observers on board the next eight long-haul shipments of sheep, in a bid to avoid further animal welfare scandals.

"At this point in time, we are very concerned the Department is making decisions that do not reflect the gravity of the situation or the seriousness of the risks to animal health and welfare," the organisation's chief scientist Dr Bidda Jones argued.

"It's clear from the outpouring of concern we've received from the public that they no longer trust the regulator to act to protect the welfare of exported animals.

"That's why the RSPCA is stepping up to provide this important oversight."

The organisation said it had many staff capable and qualified in assessing animal welfare.

Dr Jones alleged other live export ships crowded with sheep had left port while the Awassi Express had been blocked from beginning its journey to the Middle East.