The WA live export industry has suffered another blow after revelations a crippled ship anchored off Fremantle with 5240 cattle on board suffered a mechanical failure last year that caused an animal welfare disaster.

Livestock producers and exporters had been hoping for a strong revival in the trade under the new Federal Government, but the latest scare has renewed calls for the industry to be phased out.

The Pearl of Para has been in Cockburn Sound for the past two nights after abandoning a voyage to Israel because of propeller shaft coupling trouble.

A mechanical failure on the ship last year led to the death of 400 pregnant cattle on a voyage from the US to Russia.

RSPCA chief executive Heather Neil said the animals reportedly suffered a horrific death, suffocating on ammonia fumes after the ventilation system failed.

The Australian Livestock Exporters' Council and the Department of Agriculture, Fisheries and Forestry said the latest problem had not affected the ventilation system and the cattle remained in good condition with plenty of food and water.

Ms Neil urged the Government to strengthen live export regulations and to focus on boxed meat exports.

"The live export trade is a very risky business and when it goes wrong, it is usually animals that pay the price," she said. "The only way to manage the risks is by strong government regulation and developing alternatives."

Ms Neil said it was encouraging to see the Australian Agricultural Company and Kimberley pastoralist Jack Burton building abattoirs in the far north and live export companies investing in abattoirs in the south of WA.

The Marshall Islands registered Pearl of Para left Fremantle last Wednesday on a scheduled three-week voyage to Israel, a market worth $41 million to WA live cattle exporters in 2012-13.

The captain turned back after three days at sea and anchored in Cockburn Sound on Monday night. Engineers boarded the vessel yesterday to assess the time it will take to repair.

ALEC chief executive Alison Penfold said the ship was not accredited or involved in the Australian industry at the time of last year's cattle deaths.

Ms Penfold said that following a major upgrade of the ventilation and bilge pump systems, it was compliant with Australian regulations and had received a Certificate for the Carriage of Livestock issued by the Australian Maritime Safety Authority.

It was chartered by AH & R Schmidt to ship the cattle to Israel. Alan Schmidt, a veteran livestock exporter but a new player in the WA live trade, could not be contacted yesterday. The cattle remain on board the Pearl of Para. A decision on whether to continue the voyage depends on the time-frame for the repairs.