Inspector alleges sheep unable to lie down without being trampled but federal department of agriculture says conditions comply with Australian standards • Sign up to receive the top stories in Australia every day at noon

This article is more than 2 years old

This article is more than 2 years old

The federal department of agriculture says a live export ship that departed Fremantle with 75,000 sheep on board has complied with Australian standards, despite the Western Australian government describing conditions on board as “serious cause for concern”.

An inspector from the WA department of agriculture inspected the Livestock Shipping Services (LSS) ship Maysora on 11 April, shortly before it left Fremantle bound for Turkey.

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The Maysora was the first live export ship to leave Fremantle after the release of whistleblower footage showing shocking conditions aboard five voyages from Fremantle to the Middle East in 2017, including a voyage on the Awassi Express in which 2,400 sheep died from heat stress.

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The inspector alleged that the sheep were crowded into pens and unable to lie down without being trampled. They also said many water troughs were either empty or dirty with faeces, and suggested some may have died.

In a statement to Guardian Australia on Tuesday, a spokesman from the federal department of agriculture said conditions reported by the WA inspector did not reflect conditions on the rest of the voyage.

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“The majority of issues identified by the WA inspector were witnessed at the time a large volume of animals were being loaded on to the vessel for departure and do not reflect the conditions maintained on the voyage,” he said.

The spokesman said the federal department received a copy of the WA report, which included photographs and video, on Friday.

He said all the issues raised had been investigated by the independent vet on board the ship.

“The department has confirmed that the health and welfare of animals on board is being maintained in accordance with the required Australian standards,” he said.

The federal department said it was receiving reports, videos and photos of conditions on board during the three-week voyage, which is still ongoing. It said water was “clean and in plentiful supply” and only one animal was injured in loading.

The WA agriculture minister, Alannah MacTiernan, said the vet did not participate in the WA inspection.

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The independent vet was appointed by the federal department of agriculture. An independent observer was made as a condition of sail on some ships in response to heightened public concerns following the release of the whistleblower footage.

Live export ships are also required to travel with an accredited stockman, and ships to the Middle East are required to have an Australian-accredited veterinarian (AAV) on board.

Guardian Australia understands the AAV was on board when the WA inspection was conducted but the independent vet was not.

On Monday, MacTiernan said WA had received legal advice since the Maysora departed suggesting that state animal welfare laws could be used to block a live export ship from leaving port if conditions on board suggest “there is real risk of harm to animals.”

“The findings of the inspection report from the Maysora remain a serious cause for concern; we await a formal response from the federal government to these concerns,” she said.

The federal agriculture minister, David Littleproud, said he would “welcome cooperation with minister MacTiernan on this issue going forward”.

MacTiernan previously warned the live export industry that WA would use its animal welfare laws to prosecute exporters if animals were exposed to “unnecessary harm”.

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WA began investigating Emanuel Exports under the Animal Welfare Act (WA) in March over the August 2017 Awassi Express voyage.

The Awassi was due to depart for the Middle East again on 10 April but was barred from sailing by the Australian Maritime Safety Authority, which demanded improvements to the ventilation and feeding systems to bring the ship up to code.

It was finally cleared for sail on Monday after three weeks of upgrades including installing an automatic watering system to all pens and improving the ventilation system, and is due to be loaded with livestock and depart for the Middle East later in the week.