Australia’s biggest sheep exporter is under criminal investigation over conditions onboard its Middle East-bound vessels.

Perth-based Emanuel Exports has been ordered by the department of agriculture to “show cause” why it should hold an export licence.

The department on Friday also said a criminal investigation has been launched in response to footage released by Animals Australia showing sheep in horrific conditions onboard ships heading to the Middle East during the northern hemisphere summer.

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A department spokeswoman said there were allegations of overstocking, failing to have sufficient food and water available, animal injury and illness not being treated, and accredited vets and stockmen leaving vessels prior to unloading.

A number of witnesses are being questioned.

Western Australia’s agriculture minister, Alannah MacTiernan, said the investigation was “a long overdue exercise of responsibility” by the federal government.

“They have for so long allowed bad conduct in the industry to go unpunished,” she said.

MacTiernan also called on the Turnbull government to release export licence documents to help the state Labor government’s pursuit of legal action against Emanuel Exports. She has argued it was unacceptable that the government had been hiding behind commercial confidentiality.

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Emanuel Exports deferred comment to the Australian Livestock Exporters’ Council.

A spokesman said it was not appropriate to comment while the investigation is under way, other than to say the company had always been fully co-operative and compliant with requests and actions from the regulator.

Lawyers for the company have reportedly returned a lengthy submission to the “show cause” notice.