West Australian MPs have been accused of "sabre rattling" against the live export trade as a ship at the centre of an industry furore prepares to set sail without any animals on board.

The Awassi Express has been held up in Fremantle Port for about three weeks since a footage showing a voyage to the Middle East on which 2400 sheep died in their own filth amid stifling heat was broadcast across the nation.

But Pastoralists and Graziers Association WA president Tony Seabrook said there was nothing structurally wrong with the Awassi and it had an "impeccable" record excluding the August 2017 shipment.

The Awassi was on Tuesday cleared to transport livestock by the Australian Maritime Safety Authority after being ordered to improve its ventilation system.

"There is a group of very dedicated people here who are not dealing with facts, they're dealing with emotions," Mr Seabrook told ABC radio on Friday.

The Awassi will now head to northern WA to pick up cattle bound for South East Asia while Emanuel Exports will instead use the Al Messilah to transport sheep to the Middle East.

More than 3000 sheep died from extreme heat onboard the Al Messilah in 2016, when it had also been chartered by Emanuel Exports.

Mr Seabrook called on WA politicians to "butt out" of the debate and let the Commonwealth conduct its review into the northern hemisphere summer live export trade.

He accused the state's Agriculture Minister Alannah MacTiernan of "meddling" in a federal issue.

Mr Seabrook said farmers wanted a transparent industry that they could be proud of but people in the trade were "very, very nervous."

A ban on live trade would "destroy" northern Australia, he said.

WAFarmers president Tony York said exporters would be put off buying new stock as a result of the turmoil.

"It will also add costs to their businesses by way of more feed, and possibly reduce demand and prices in markets," Mr York said.