The company behind the disastrous Awassi Express voyage on which thousands of sheep died says it will appeal the federal Agriculture Department’s decision to cancel its export licence.

The department suspended Emanuel Exports’ licence in June after footage was broadcast of thousands of sheep dead, dying and suffering in sweltering conditions on a ship bound for the Middle East.

The decision to cancel the Perth-based company’s licence late on Tuesday followed “a thorough investigation and show cause process” and was “not one taken lightly”, the department said in a statement.

“The department has … taken action against this company in the best interests of the industry and for the protection of Australia’s high standards of animal welfare and health,” the statement read.

The company, which has been exporting to the Middle East since 1963, said on Wednesday it would appeal the decision to the Administrative Appeals Tribunal.

“We will appeal this notice as a matter of priority,” director Nicholas Daws said.

“Emanuels remains committed to maintaining the highest animal welfare standards.”

Pastoralists and Graziers Association president Tony Seabrook responded angrily to the cancellation, saying the only winners were animal welfare activists, but WAFarmers president Tony York said critics of the trade could take comfort the regulator was doing its job.

RSPCA Australia senior policy officer Jed Goodfellow welcomed the cancellation, adding the community “should be under no illusion that Emanuel was a rogue operator or an outlier”.

The Awassi footage sparked a national debate about the future of the industry and resulted in the department imposing tighter regulations on exporters.

Australian sheep shipments to the Middle East ground to a complete halt this northern summer because the other major company servicing that market, Livestock Shipping Services, voluntarily switched its focus to South America.

WA Agriculture Minister Alannah MacTiernan said the state government supported “any steps to weed out dodgy live export operators and clean up the trade”.

But the federal government had handled the sector badly for a long time so sheep farmers and processors should receive a financial assistant package to help them adjust to their sudden “new reality”, Ms MacTiernan said.

An Emanuel spokesman told AAP almost all of the 60,000 sheep that were left stranded in a Perth feedlot after the company’s licence was suspended have been sold at abattoirs.